The Artemis Manual

Copyright 1999-2014 by Genome Research Limited This document describes release 1 o! "rtemis a #$" se%uence &ie'er and se%uence annotation tool( "rtemis is !ree so!t'are) you can redistribute it and*or modi!y it under the terms o! the G$+ General ,ublic License as published by the -ree .o!t'are -oundation) either &ersion 2 o! the License/ or 0at your option1 any later &ersion( This program is distributed in the hope that it 'ill be use!ul/ but 23T45+T "$6 2"RR"$T6) 'ithout e&en the implied 'arranty o! 78RC4"$T"93L3T6 or -3T$8.. -5R " ,"RT3C+L"R ,+R,5.8( .ee the G$+ General ,ublic License !or more details( 6ou should ha&e recei&ed a copy o! the G$+ General ,ublic License along 'ith this program) i! not/ 'rite to the -ree .o!t'are -oundation/ 3nc(/ :9 Temple ,lace/ .uite ;;0/ 9oston/ 7" 02111-1;0< +." -or the !ull te=t o! the license see the section called Copyright Notice in Chapter 1(

Table of Contents 1( 3ntroduction to "rtemis 2hat is "rtemis> .ystem Re%uirements Getting and 3nstalling "rtemis 3nstalling ?a&a 3nstallation 3nstructions !or +$3@ and G$+*Linu= 3nstallation 3nstructions !or 7ac5.@ 3nstallation 3nstructions !or 2indo's .e%uence and "nnotation -ile -ormats Concepts The A8ntryA 879L*GenbanB -eatures 879L*GenbanB -eature Ceys 879L*GenbanB -eature Duali!iers ATabA -iles or ATableA -iles The "cti&e 8ntries The #e!ault 8ntry -eature .egments The .election -eature Colours Contributions and .uggestions #istribution Conditions and "cBno'ledgments Copyright $otice 2( .tarting "rtemis Running "rtemis on +$3@ and G$+*Linu= .ystems +$3@ Command Line "rguments !or "rtemis -options -Xmsn -Xmxn -Dblack_belt_mode=false -Doffset=10000 -Duserplot=pathToFile -Dloguserplot=pathToFile -Dbam=pathToFile

-Dbam1=pathToFile1 -Dbam2=pathToFile2 -Dbam lone=n -Dsho!_snps -Dsho!_snp_plot -Dsho!_co"_plot -Dchado=#hostname$port%database&username# -Dread_onl' -Dsho!_for!ard_lines=false -Dsho!_re"erse_lines=false Running "rtemis on 7acintosh .ystems Running "rtemis on 2indo's .ystems The "rtemis Launch 2indo' The -ile 7enu The 5ptions 7enu ;( The "rtemis 7ain 2indo' 5&er&ie' o! the 8ntry 8dit 2indo' " breaBdo'n o! the main "rtemis edit 'indo' The -ile 7enu .ho' -ile 7anager ((( Read "n 8ntry ((( Read 8ntry 3nto Read 9"7 * EC- ((( .a&e #e!ault 8ntry .a&e "n 8ntry .a&e "n 8ntry "s .a&e "ll 8ntries 2rite Clone This 2indo' .a&e "s 3mage -iles 0png*s&g1 ,rint ,rint ,re&ie' ,re!erences Close The 8ntries 7enu .et $ame 5! 8ntry .et #e!ault 8ntry Remo&e "n 8ntry Remo&e "cti&e 8ntries #eacti&ate "ll 8ntries The .elect 7enu -eature .elector ((( "ll "ll 9ases .elect "ll -eatures in $on-matching Regions $one 9y Cey C#. -eatures .ame Cey 5pen Reading -rame -eatures 5&erlapping .election -eatures 2ithin .election 9ase Range ((( -eature "" Range ((( Toggle .election The Eie' 7enu .elected -eatures .election

.earch Results C#. Genes "nd ,roducts -eature -ilters 5&er&ie' -or'ard .trand 5&er&ie' Re&erse .trand 5&er&ie' -eature 9ases -eature 9ases "s -".T" -eature "mino "cids -eature "mino "cids "s -".T" -eature .tatistics -eature ,lots The Goto 7enu $a&igator ((( .tart o! .election 8nd o! .election -eature .tart -eature 8nd .tart o! .e%uence 8nd o! .e%uence -eature 9ase ,osition ((( -eature "mino "cid ((( The 8dit 7enu +ndo Redo .elected -eatures in 8ditor .ubse%uence 0and -eatures1 -ind 5r Replace Duali!ier Te=t Duali!ier0s1 o! .elected -eature .elected -eature0s1 7o&e .elected -eatures To Copy .elected -eatures To Trim .elected -eatures 8=tend .elected -eatures -i= .top Codons "utomatically Create Gene $ames -i= Gene $ames 9ases Contig Reordering ((( 4eader 5! #e!ault 8ntry The Create 7enu $e' -eature -eature -rom 9ase Range 3ntergenic -eatures -eatures -rom $on-matching Regions $e' 8ntry 7arB 5pen Reading -rames ((( 7arB 8mpty 5R-s ((( 7arB 5pen Reading -rames 3n Range ((( 7arB -rom ,attern ((( 7arB "mbiguities The Run 7enu Con!iguring the Run 7enu The Graph 7enu 4ide "ll Graphs "dd +sage ,lots (((

"dd +ser ,lot ((( GC Content 0F1 GC Content 0F1 2ith 2(: .# Cuto!! "G Content 0F1 GC -rame ,lot Correlation .cores Re&erse Correlation .cores GC #e&iation 0G-C1*0GGC1 "T #e&iation 0"-T1*0"GT1 Carlin .ignature #i!!erence Cumulati&e "T .Be' and Cumulati&e GC .Be' ,ositional "symmetry 3n!ormational 8ntropy .caled Chi .%uare 7utational Response 3nde= 8!!ecti&e Codon $umber 3ntrinsic Codon #e&iation 3nde= The #isplay 7enu .ho' 8ntry 9uttons .ho' 9ase Eie' .ho' -eature List The 8ntry 9utton Line The 5&er&ie' and #$" Eie's Changing the .election !rom a Eie' 2indo' 5ther 7ouse Controlled -unctions The ,op-up 7enu .crolling The Eie' Changing The .cale A#irect 8ditingA The -eature List Changing the .election !rom the -eature List 5ther 7ouse Controlled -unctions The ,op-up 7enu .crolling The List Graphs and ,lots "nnotation Ealidation 4o' to Run Ealidation ChecBs Ealidation ChecBs -or "ll -ile Types Ealidation ChecBs -or G--; Ealidation Report $otes on +sing The 7ouse 4( ,roHect -ile 7anager 5&er&ie' +sing the ,roHect -ile 7anager :( .ecure .hell 0..41 ,lugin To "rtemis 5&er&ie' o! the ..4 ,lugin Login 3n .etting up a ..4 tunnel +sing ,utty to .et +p " Tunnel +sing the ..4 connection to run -asta and 9L".T Con!iguring .earches to be run &ia ..4 ( "rtemis Con!iguration 5ptions The 5ptions -ile "rtemis 5ption #escriptions font_si(e font_name

base_plot_height feature_plot_height dra!_feature_borders sho!_for!ard_lines sho!_re"erse_lines dra!_feature_arro!s o"er"ie!_feature_labels o"er"ie!_one_line_per_entr' sho!_list sho!_base_"ie! features_on_frame_lines frame_line_features feature_labels one_line_per_entr' genetic_codes translation_table_1 extra_ke's extra_)ualifiers common_ke's h'perlinks undo_le"els minimum_orf_si(e direct_edit feature_dna_programs feature_protein_programs ncbi_dna_search ncbi_protein_search .etting Colours 5ptions -or ,lots and Graphs 5ptions -or " Chado #atabase 5ptions -ile -ormat "n 8=ample 5ptions -ile List of Tables ;-1( 3+9 9ase Codes

Chapter 1. Introduction to Artemis What is Artemis?

"rtemis is a #$" se%uence &ie'er and annotation tool that allo's &isualisation o! se%uence !eatures and the results o! analyses 'ithin the conte=t o! the se%uence/ and its si=-!rame translation( "rtemis is 'ritten in ?a&a/ reads 879L or G8$9"$C !ormat se%uences and !eature tables/ and can 'orB on se%uences o! any siIe( 5n +ni= and G$+*Linu= systems/ gi&en an 879L accession number "rtemis also can read an entry directly !rom the 893 using #b!etch( This !eature is still e=perimental/ but copes 'ell 'ith straight!or'ard entries 0see the section called Open from EBI - Dbfetch ... in Chapter 21( -or more in!ormation on "rtemis go to the "rtemis 'eb pages(

System Re uirements
"rtemis 'ill run on any machine that has a recent &ersion o! ?a&a( This &ersion o! "rtemis re%uires ?a&a 1( at least( 7ost o! the de&elopment has been done using ?#C &1( and some o! the more ad&anced !eatures 09amEie' and EC-*9C- Eie'1 re%uire ?a&a 1( or higher( .ee the section called Getting and Installing Artemis !or details on ho' to get ?a&a(

!ettin" and Installin" Artemis

The most up to date &ersion o! "rtemis is al'ays a&ailable !rom the "rtemis 'eb pages(

Installin" #a$a
9e!ore installing "rtemis you 'ill need to maBe sure you ha&e ?a&a installed( Linu=/ +$3@ users should get the current ?a&a &ersion !rom the 5racle( 2indo's users should get latest stable release !rom ?a&a &ersion !rom 5racle( 5n some &ersions o! 2indo's 0such as 2indo's 20001 you 'ill need be ha&e administrator pri&ileges !or your machine to success!ully install ?a&a( 7acintosh users 'ith 7ac5. @ should ha&e ?a&a installed( 6ou can get the latest ?a&a 1( &ersion !rom "pple( ?a&a < !or 3ntel 7ac running 7ac 5.@ 10(<(; or abo&e can be do'nloaded !rom 5racle(

Installation Instructions for %&I' and !&%(Linu)

Change directory to the directory you 'ish to install "rtemis in( 2e 'ill use *% in this e=ample and in the ne=t chapter( uncompress and untar the artemis_compiled+tar+g( !ile( 5n +$3@ the command isJ tar *)f artemis+compiled.tar."* This 'ill create a directory called *%artemis 'hich 'ill contain all the !iles necessity !or running "rtemis( -or instructions on ho' to run "rtemis on +$3@ and G$+*Linu= once the archi&e is unpacBed see the section called R nning Artemis on !NI" and GN!#$in % &ystems in Chapter 2(

Installation Instructions for Mac,S'

-or 7ac5.@ users an archi&e artemisKact(dmg(gI disB image is pro&ided( This contains both "rtemis and "CT applications( This can be uncompressed using gunIipJ gun(ip artemis_act+dmg+g( "lternati&ely on 5. @ an easier solution is pro&ided by .tu!!3t 8=pander( #ouble-clicB on any !ile ending in A(gIA and .tu!!3t 8=pander 'ill be launched to uncompress that !ile(

The uncompressed disB image !ile AartemisKact(dmgA can be mounted by double clicBing on it( The mounted image/ AartemisKactA/ can then be opened and the so!t'are contents displayed by double clicBing on it( 5pen an read the AReadme(t=tA !ile(

Installation Instructions for Windo-s

5n 2indo's systems 'ith ?a&a 0&ersion 1( or higher1/ installing "rtemis is as simple as do'nloading the the artemis(Har !ile to an appropriate place 0such as the desBtop or the ,rograms !older1( 2hen do'nloading some &ersions o! 'indo's mistaBe this !ile !or a Iip !ile ensure it does not name this artemis(Iip/ i! it does rename it to artemis(Har 0#5 $5T +$L3, T43. -3L81( -or instructions on ho' to run "rtemis on 2indo's once it is unpacBed see the section called R nning Artemis on 'indo(s &ystems in Chapter 2 (

Se uence and Annotation .ile .ormats

"rtemis reads in the common se%uence and annotation !ile !ormats( "s larger data sets become more common it is no' possible to inde= some o! these !ormats 0-".T" and G--;1 to speed up and impro&e the per!ormance o! "rtemis( "rtemis can read the !ollo'ing se%uence and annotation !ile !ormats( "s discussed in the ne=t section these can be read indi&idually or as a combination o! di!!erent annotation !iles being read in and o&erlaid on the same se%uence( 879L !ormat( Gen9anB !ormat( G--; !ormat( The !ile can contain both the se%uence and annotation or the G-- can Hust be the !eature annotation and be read in as a seperate entry and o&erlaid onto another entry containing the se%uence( -".T" nucleotide se%uence !iles can be one o! the !ollo'ingJ .ingle -".T" se%uence( 7ultiple -".T" se%uence( The se%uences are concatenated together 'hen opened in

"rtemis( 3nde=ed -".T" !iles can be read in( The !iles are inde=ed using ."7toolsJ
samtools faidx ref+fasta

" drop do'n menu o! the se%uences in the 8ntry toolbar 0see the section called A brea)do(n of the main Artemis edit (indo( in Chapter ;1 at the top can then used to select the se%uence to &ie'( 3nde=ed G--; !ormat( This can be read in and o&erlaid onto an inde=ed -".T" !ile( The inde=ed G--; !ile contains the !eature annotations( To inde= the G-- !irst sort and bgIip the !ile and then use tabi= 'ith A-p g!!A option 0see the tabi= manual1J
,grep -#.# in+gff/ grep -" -#.# in+gff 0 sort -k111 -k212n3 0 bg(ip 4 sorted+gff+g(/ tabix -p gff sorted+gff+g(

" drop do'n menu o! the se%uences in the 8ntry toolbar 0see the section called A brea)do(n of the main Artemis edit (indo( in Chapter ;1 at the top can then used to select the se%uence to &ie'( +sing inde=ed -".T" and inde=ed G-- !iles impro&es the memory management and enables large genomes to be &ie'ed( $ote that as it is inde=ed the se%uence and annotation are read-only and cannot be edited( 2hen there are many contigs to select !rom it can be easier to display the one o! interest by typing the name into the drop do'n list( The output o! MS/crunch( MS/crunch must be run 'ith the 0) or 0d !lags( The output o! blastall &ersion 2(2(2 or better( blastall must be run 'ith the 0m 1 !lag 'hich generates one line o! in!ormation per 4.,( $ote that currently "rtemis displays each 9last 4., as a separate !eature rather than displaying each 9L".T hit as a !eature(

Concepts
4ere are some general concepts about "rtemis that may maBe the rest o! this manual clearer(

The 23ntry2
"n AentryA in "rtemis-speaB is not necessarily a complete 879L or G8$9"$C entry( 3n most places in this manual 'hen 'e re!er to an entry 'e mean a !ile that contains Hust the !eature table lines 0the FT lines1 o! an 879L*G8$9"$C entry 0see the section called *+ab* ,iles or *+able* ,iles1( "!ter loading a se%uence and opening an entry edit 'indo' 0see the section called Open ... in Chapter 21 it is then possible to o&erlay many !eature tables 0see the section called Read An Entry ... in Chapter ;1( 8ach o! these !eature table !iles is called an entry by "rtemis and itMs !eatures are Bept separate !rom those o! other entries( This meaning o! the 'ord AentryA is used by most o! the items in the -ile menu 0see the section called +he ,ile -en in Chapter ;1 and by the items in the 8ntry menu 0see the section called +he Entries -en in Chapter ;1(

3M4L(!enban5 .eatures
" A!eatureA in an 879L or GenbanB !ile is a region o! #$" that has been annotated 'ith a Bey*type 0see the section called E-B$#Genban) ,eat re .eys 1 and Iero or more %uali!iers 0see the section called E-B$#Genban) ,eat re / alifiers 1( 3n an 879L or GenbanB !ormated !ile the !eatures o! a piece o! #$" are listed in the !eature table section 0see the section called *+ab* ,iles or *+able* ,iles1(

3M4L(!enban5 .eature 6eys

"ll 879L and GenbanB !eatures ha&e e=actly one ABeyA assigned to them( The Bey is the type o! the !eature( 8=amples include D5 0a oDing 5e%uence1/ intron and misc_feature 0675 ellaneous feature1( The 893 has a list o! all possible !eature Beys(

3M4L(!enban5 .eature 7ualifiers

The %uali!iers o! a !eature in an 879L or GenbanB !ile are the notes and e=tra in!ormation about the !eature( -or e=ample an exon !eature might ha&e a %gene=#rat # %uali!ier/ meaning that the e=on !eature is part o! a gene named rat ( The 893 has a list o! all possible !eature %uali!iers(

2Tab2 .iles or 2Table2 .iles

"n 879L or GenbanB !ile that only contains a !eature table 0Hust FT lines/ no se%uence or header lines1 is called a AtableA !ile/ or sometimes Hust a AtabA !ile because the o!ten has a name liBe Asome!ile(tabA(

The Acti$e 3ntries

"ll entries in "rtemis are considered to be Aacti&eA or Ainacti&eA( The o&er&ie'/ #$" &ie' and !eature list parts o! the main 'indo' 'ill only display !eatures !rom acti&e entries( To !ind out ho' to set the acti&e and inacti&e entries see the section called +he Entries -en in Chapter ;(

The 8efault 3ntry

7any actions 0such as creating !eatures1 re%uire an entry to be identi!ied as the source or destination !or the action( .ome actions/ such as A7o&e .elected -eatures To (((A in the edit menu/ 'ill e=plicitly asB !or

an entry/ but some assume that the action re!ers to a Ade!ault entryA that 'as pre&iously set by the user( The de!ault entry can be set by using the A.et #e!ault 8ntry (((A menu item in the 8ntries menu 0see the section called &et Defa lt Entry in Chapter ;1 or by using the entry buttons 0see the section called +he Entry B tton $ine in Chapter ;1(

.eature Se"ments
The term AsegmentA in the conte=t o! a C#. !eature means Ae=onA( 2e use the term AsegmentA/ because non-C#. !eatures 0such as miscK!eature1 can ha&e e=on-liBe parts too/ but the term Ae=onA 'ould be inappropriate in that case(

The Selection
3n common 'ith applications liBe 'ord processors and graphics programs/ "rtemis allo's the user to AselectA the obHects that the program 'ill act on( The obHects to act on in "rtemis are !eatures/ !eature segments or bases( 3! a !eature segment is added to the selection/ the !eature that contains the segment is implicitly added as 'ell( The current selection can be changed 'ith the .elect 7enu 0see the section called +he &elect -en in Chapter ;1 or using the mouse 0see the section called Changing the &election from a 0ie( 'indo( in Chapter ; and the section called Changing the &election from the ,eat re $ist in Chapter ;1(

.eature Colours
8ach !eature displayed in "rtemis can be gi&en a colour( The a&ailable colours are set in the options !ile 0see Chapter 1 and are assigned to a !eature by adding a %colour %uali!ier 0see the section called &elected ,eat res in Editor in Chapter ;1( Currently there are t'o 'ays o! speci!ying !eature colours( The !irst 'ay uses a single number( -or e=ample red is colour 2/ so adding %colour=2 as a !eature %uali!ier 'ill maBe that !eature red( The second 'ay is to speci!y the red/ green and blue components o! the colour( 8ach o! the components can taBe &alues !rom 0 to 2::/ 'ith 2:: being the most intense( -or e=ample %colour=288 0 0 is another 'ay to gi&e a !eature the colour red( 3! no %colour %uali!ier is set !or a !eature a de!ault colour is used 0the de!ault colours are also speci!ied in the options !ile1(

Contributions and Su""estions

2e 'elcome contributions to "rtemis/ bug reports !rom users and suggestions !or ne' !eatures( "n email discussion list has been set up !or this purpose( To Hoin/ send a message to Martemis-usersHoinNsanger(ac(uBM 'ith Msubscribe artemis-usersM in the body 0not the subHect1( "nnouncements 'ill also be sent to this list(

8istribution Conditions and Ac5no-led"ments

"rtemis may be !reely distributed under the terms o! the G$+ General ,ublic License( .ee the section called Copyright Notice !or the !ull te=t o! the license( The de&elopment o! "rtemis is !unded by the 2ellcome TrustMs through itMs support o! the ,athogen Genomics Group at The .anger 3nstitute(

Copyri"ht &otice
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:K J>==>:TI 11+ A< >;5< TL< @=K9=>6 75 ?7 <:5<D F=<< KF L>=9<1 TL<=< 75 :K J>==>:TI FK= TL< @=K9=>61 TK TL< <XT<:T @<=67TT<D AI >@@?7 >A?< ?>J+ <X <@T JL<: KTL<=J75< 5T>T<D 7: J=7T7:9 TL< K@I=79LT LK?D<=5 >:D%K= KTL<= @>=T7<5 @=KB7D< TL< @=K9=>6 #>5 75# J7TLK;T J>==>:TI KF >:I O7:D1 <7TL<= <X@=<55<D K= 76@?7<D1 7: ?;D7:91 A;T :KT ?767T<D TK1 TL< 76@?7<D J>==>:T7<5 KF 6<= L>:T>A7?7TI >:D F7T:<55 FK= > @>=T7 ;?>= @;=@K5<+ TL< <:T7=< =75O >5 TK TL< P;>?7TI >:D @<=FK=6>: < KF TL< @=K9=>6 75 J7TL IK;+ 5LK;?D TL< @=K9=>6 @=KB< D<F< T7B<1 IK; >55;6< TL< K5T KF >?? :< <55>=I 5<=B7 7:91 =<@>7= K= K==< T7K:+ 12+ 7: :K <B<:T ;:?<55 =<P;7=<D AI >@@?7 >A?< ?>J K= >9=<<D TK 7: J=7T7:9 J7?? >:I K@I=79LT LK?D<=1 K= >:I KTL<= @>=TI JLK 6>I 6KD7FI >:D%K= =<D75T=7A;T< TL< @=K9=>6 >5 @<=67TT<D >AKB<1 A< ?7>A?< TK IK; FK= D>6>9<51 7: ?;D7:9 >:I 9<:<=>?1 5@< 7>?1 7: 7D<:T>? K= K:5<P;<:T7>? D>6>9<5 >=757:9 K;T KF TL< ;5< K= 7:>A7?7TI TK ;5< TL< @=K9=>6 ,7: ?;D7:9 A;T :KT ?767T<D TK ?K55 KF D>T> K= D>T> A<7:9 =<:D<=<D 7:> ;=>T< K= ?K55<5 5;5T>7:<D AI IK; K= TL7=D @>=T7<5 K= > F>7?;=< KF TL< @=K9=>6 TK K@<=>T< J7TL >:I KTL<= @=K9=>6531 <B<: 7F 5; L LK?D<= K= KTL<= @>=TI L>5 A<<: >DB75<D KF TL< @K557A7?7TI KF 5; L D>6>9<5+

Chapter 9. Startin" Artemis Runnin" Artemis on %&I' and !&%(Linu) Systems

5n +ni= and G$+*Linu= the easiest 'ay to run the program is to run the script called art in the "rtemis installation directory 0see the section called Getting and Installing Artemis in Chapter 11/ liBe thisJ artemis(art 3! all goes 'ell you 'ill be presented 'ith a small 'indo' 'ith three menus( .ee the section called +he Artemis $a nch 'indo( to !ind out 'hat to do ne=t( "lternati&ely you start "rtemis 'ith the name o! a se%uence !ile or embl !ile egJ artemis(art artemis(etc(c191:.embl 5r i! you ha&e a se%uence !ile and e=tra !eature table !iles you can read them all 'ith a command liBe this 0the e=ample !ile c121:(blastn(tab is the result o! a 9L".T$ search against 879L 'hich has been con&erted to !eature table !ormat1J artemis(art artemis(etc(c191:.embl ; artemis(etc(c191:.blastn.tab $ote that any number o! !eature !iles can be read by listing them a!ter the plus sign( The AGA must be surrounded by spaces( .ee the section called !NI" Command $ine Arg ments for Artemis !or a list o! the other possible arguments( "lso to see a summary o! the options typeJ artemis(art 0help

4ere is an alternati&e 'ay to run "rtemis i! the art script doesnMt 'orB !or youJ cd <(artemis =a$a 0m):>>m 0ms1>>m 0classpath lib(bio=a$a.=ar?lib(=emAli"n.=ar?lib(=9ssh(=9ssh0 core.=ar?lib(ibatis(ibatis09.@.A.B9C.=ar?lib(ibatis(lo"A=01.9.1A.=ar?lib(ibatis(c"lib0nodep0 9.9.=ar?lib(post"res l01.A0B>1.=dbc@.=ar?lib(picard.=ar?lib(picard(sam.=ar?lib(bati5(bati50a-t0 util.=ar?lib(bati5(bati50codec.=ar?lib(bati5(bati50dom.=ar?lib(bati5(bati50e)t.=ar?lib(bati5(bati50 s$""en.=ar?lib(bati5(bati50util.=ar?lib(bati5(bati50)ml.=ar?lib(commons0lan"09.C.=ar?lib(commons0 net09.9.=ar?. 08artemis.en$ironmentD%&I' u5.ac.san"er.artemis.components.ArtemisMain

%&I' Command Line Ar"uments for Artemis

"s 'ell as the listing !ile names on the command line/ the !ollo'ing s'itches are a&ailable to +$3@ usersJ

-options
This option instructs "rtemis to read an e=tra !ile o! options a!ter reading the standard options( 0.ee the section called +he Options ,ile in Chapter !or more about the "rtemis options !ile(1 -or e=ample -options +%ne!_options 'ill instruct "rtemis to read ne!_options in the current directory as an options !ile(

-Xmsn -Xmxn
+se -Xmsn to speci!y the initial siIe/ in bytes/ o! the memory allocation pool( This &alue must be a multiple o! 1024 greater than 179( "ppend the letter B or C to indicate Bilobytes/ or m or 7 to indicate megabytes( +se -Xmxn to speci!y the ma=imum siIe/ in bytes/ o! the memory allocation pool( This &alue must a multiple o! 1024 greater than 279( "ppend the letter B or C to indicate Bilobytes/ or m or 7 to indicate megabytes(

-Dblack_belt_mode=false
3! this is set to !alse then 'arning messages are Bept to a minimum(

-Doffset=10000
This sets the base position that "rtemis opens at/ e(g( 10000(

-Duserplot=pathToFile
This can be used to open userplots !rom the command line( The paths are comma separated to open multiple plots 0-#userplotOM*pathTo-ile*user,lot1/*pathTo-ile*user,lot2M1(

-Dloguserplot=pathToFile
This is the same as the abo&e userplot option e=cept that the log trans!orm o! the data is plotted(

-Dbam=pathToFile
This can be used to open 9"7 !iles and*or EC-*9C- !iles 0see the section called Read BA- # 0C, ... in Chapter ; !or more about the using these !ile types1( This can taBe a path name to a !ile or an 4TT, address(

-Dbam1=pathToFile1 -Dbam2=pathToFile2
The !ollo'ing 'ill open 9"7 !iles in separate panels 0using -#bamP1/2/;(((Q1J art 08bam1DfileA.bam 08bam9Dfile4.bam

-Dbam lone=n
7ultiple 9"7 panels can be opened using the bamClone !lag this is used 'ith the -#bam !lagJ art 08bamDE(pathTo.ile(file1.bamF(pathTo.ile(file9.bamE 08bamCloneDn 0'here n is an integer greater than 11( "ll 9"7 !iles are then sho'n in each panel(

-Dsho!_snps
.ho' .$, marBs in 9"7 panels(

-Dsho!_snp_plot
"utomatically open .$, plots !or 9"7 !iles that are opened(

-Dsho!_co"_plot
"utomatically open co&erage plots !or 9"7 !iles that are opened(

-Dchado=#hostname$port%database&username#
This is used to get "rtemis to looB !or the database( The address o! the database 0hostname/ port and name1 can be con&eniently included 0e(g( -#chadoOAgenedb-db(sanger(ac(uBJ:4;2*snapshot>genedbKroA1 and these details are then the de!ault database address in the popup login 'indo'(

-Dread_onl'
-or a read only chado connection -#readKonly is speci!ied on the command line 0e(g( art -#chadoOAgenedb-db(sanger(ac(uBJ:4;2*snapshot>genedbKroA -#readKonly1(

-Dsho!_for!ard_lines=false
4ide*sho' !or'ard !rame lines(

-Dsho!_re"erse_lines=false
4ide*sho' re&erse !rame lines(

Runnin" Artemis on Macintosh Systems

5n 7ac5.@ machines "rtemis can be started by double clicBing on the "rtemis icon( The icon can be added to the docB by dragging it !rom a M-inderM 'indo' and dropping it onto the position in the docB you 'ant it( 3n addition se%uence !iles 0'ith g!!/ embl/ 879L/ genbanB/ gbB/ !asta/ se%/ art !ile name e=tensions1 can be dragged and dropped on to the "rtemis application image to open them up( To change the memory allocated to "rtemis on 7ac5.@/ set the &alue in the !ile 3n!o(plist in the directory "rtemis(app*Contents( To'ards the bottom o! the !ile there are a couple o! lines that looB liBe thisJ

Qke'4B6KptionsQ%ke'4 Qstring4-XmxE00mQ%string4

Changing the &alue a!ter -@m= 'ill change the memory used by "rtemis(

Runnin" Artemis on Windo-s Systems

5n systems 'ith ?a&a 1( 0or abo&e1 installed "rtemis can be started by double clicBing on the artemis(Har icon(

The Artemis Launch WindoThis is the !irst 'indo' that opens 'hen you start "rtemis( The menus at the top o! this 'indo' allo' you to read a ne' se%uence or embl entry(

The .ile Menu

,pen /ro=ect Mana"er ...
This opens up the ,roHect -ile 7anager 'hich can be used to !acilitate launching o! groups o! !iles 0annotation/ userplot/ 9"7/ EC-1 'ith a particular se%uence( .ee Chapter 4(

,pen .ile Mana"er ...

.electing this sho's the !iles and directories that are in the directory "rtemis is launched !rom( The user home directory and the current 'orBing directories are sho'n and can be na&igated(

,pen SSG .ile Mana"er ...

This opens a 'indo' displaying a local !ile manager at the top and login options to access a remote !ile system &ia .ecure .hell 0..41( 2hen the login details are typed in and MConnectM pressed the bottom hal! o! the 'indo' 'ill display the other 0remote1 !ile system( .ee Chapter : to !ind out ho' to use this and ho' to set up the connection(

,pen ...
3! you select this menu item a !ile re%uester 'ill be displayed 'hich allo's you to open a !lat !ile containing an entry( 3! the !ile you select is success!ully read a ne' 'indo' 'ill open/ 'hich sho's the

se%uence and !eatures !or the entry( .ee Chapter ; to !ind out ho' to use the main 'indo'(

,pen from 34I 0 8bfetch ...

The !unctions 'ill asB the user !or an accession number and then 'ill attempt to read it directly !rom the 893 using #b!etch( 3! all goes 'ell you 'ill be presented 'ith an &ie'*edit 'indo' 0see Chapter ;1(

7uit
This menu item 'ill close all 'indo's and then e=it the program

The ,ptions Menu

Re0read ,ptions
Choosing this menu item 'ill discard the current options settings and then re-read the options !ile( $ote that changing the !ont siIe in the !ile and then selecting this menu item 'ill only change the !ont siIe !or ne' 'indo's/ not e=isting 'indo's( Currently some options are una!!ected by this menu item( .ee the section called Options ,ile ,ormat in Chapter !or more in!ormation about options(

3nable 8irect 3ditin"

This menu item 'ill toggle Adirect editingA option( 3t is o!! be de!ault because it can ha&e surprising results unless the user is e=pecting it( .ee the section called *Direct Editing* in Chapter ; !or more detail about this(

!enetic Code Tables

These options maBe all the $C93 Genetic Codes a&ailable( The de!ault setting is the .tandard Code( This setting e!!ects the display o! start codons 0see the section called &tart Codons in Chapter ;1 and the A.uspicious .tart Codons (((A !eature !ilter 0see the section called & spicio s &tart Codons ... in Chapter ;1(

Send Searches Hia SSG

This is an ad&anced option !or sites that ha&e set up the ability to submit searches &ia ..4 to another machine(

4lac5 4elt Mode

This is an ad&anced option that can be used to turn o!! 'arning message( This options is displayed i! the Ha&a property 0blacBKbeltKmode1 is speci!ied on opening up "rtemis/ i(e( art -#blacBKbeltKmodeOyes(

Gi"hli"ht Acti$e 3ntry

2hen this option is on and the A5ne Line ,er 8ntryA is on 0see the section called One $ine 1er Entry in Chapter ;1 the line that the acti&e entry is on 'ill be highlighted in yello'(

Sho- Lo" Windo.ho' the log o! in!ormational messages !rom "rtemis( Currently the log 'indo' is only used on +$3@ and G$+*Linu= systems to sho' the output o! e=ternal programs( This menu item is only a&ailable 'hen running "rtemis on +$3@ or G$+*Linu= systems( The logging is controlled by log4H( The log4H(properties !ile 0etc*log4H(properties in the source distribution1 sets the le&el o! logging( This can be used to send the logging in!ormation to other places such as a !ile(

Gide Lo" Windo4ide the log o! in!ormational messages( This menu item is only a&ailable 'hen running "rtemis on +$3@ or G$+*Linu= systems(

Chapter @. The Artemis Main Windo,$er$ie- of the 3ntry 3dit WindoThis 'indo' is the main editing and &ie'ing 'indo'( .ee the section called Open ... in Chapter 2 or the section called Open from EBI - Dbfetch ... in Chapter 2 to !ind out ho' to read an entry 0and hence open one o! these 'indo's1( The !ollo'ing images sho' a breaBdo'n o! the main "rtemis edit 'indo'( The !ull screen shot is here(

A brea5do-n of the main Artemis edit -indo1( 2( ;( 4(

:(

CeyJ 1( The menus !or the main 'indo' 0described later in this chapter1( 2( " one line summary o! the current selection 0see the section called +he &elect -en and the section called +he &election in Chapter 1 !or more1( ;( This line contains one button !or each entry that has been loaded( These buttons allo' the user to set the de!ault entry 0see the section called +he Defa lt Entry in Chapter 11 and to set the acti&e entries 0see the section called +he Acti2e Entries in Chapter 11( -or more detail on operating the buttons see the section called +he Entry B tton $ine(

4( This sho's an o&er&ie' o! the se%uence and the !eatures !rom the acti&e entries( 0see the section called +he O2er2ie( and DNA 0ie(s1( :( This is called the A#$" &ie'A to distinguish it !rom the o&er&ie'/ but in !act it operates in a &ery similar 'ay( 0see the section called +he O2er2ie( and DNA 0ie(s1( ( " te=tual summary o! the acti&e !eatures( 0.ee the section called +he ,eat re $ist1(

The .ile Menu

7ost o! the items in this menu are used to read and 'rite entries and parts o! entries/ the e=ceptions are Clone and Close(

Sho- .ile Mana"er ...

This 'ill open the !ile manager/ or i! it is already open 'ill bring it to the !oreground( 8ntries can be dragged !rom the !ile manager into the artemis main 'indo' and dropped( 2hen dropped the entry is then read in and displayed(

Read An 3ntry ...

Read an entry 0see the section called +he *Entry* in Chapter 11/ but Beep it separate !rom the others( " ne' button 'ill be created on the entry button line !or the ne' entry( The ne' entry 'ill be marBed as acti&e 0see the section called +he Acti2e Entries in Chapter 11 and 'ill be the ne' de!ault entry 0see the section called +he Defa lt Entry in Chapter 11( .ee the section called &e3 ence and Annotation ,ile ,ormats in Chapter 1( This !unction only reads the !eature section o! the input !ile - the se%uence 0i! any1 is ignored(

Read 3ntry Into

Read the !eatures !rom an entry 0see the section called +he *Entry* in Chapter 11 chosen by the user and then insert them into the entry selected by the user(

Read 4AM ( HC. ...

"rtemis can read in and &isualise 9"7/ EC- and 9C- !iles( These !iles need to be inde=ed as described belo'( They re%uire "rtemis to be run 'ith at least ?a&a 1( ( .ome e=amples can be !ound on the "rtemis homepage( 9"7 !iles need to be sorted and inde=ed using ."7tools( The inde= !ile should be in the same directory as the 9"7 !ile( This pro&ides an integrated 9amEie' panel in "rtemis/ displaying se%uence alignment mappings to a re!erence se%uence( 7ultiple 9"7 !iles can be loaded in !rom here either by selecting each !ile indi&idually or by selecting a !ile o! path names to the 9"7 !iles( The 9"7 !iles can be read !rom a local !ile system or remotely !rom an 4TT, ser&er( 9amEie' 'ill looB to match the length o! the se%uence in "rtemis 'ith the re!erence se%uence lengths in the 9"7 !ile header( 3t 'ill display a 'arning 'hen it opens i! it !inds a matching re!erence se%uence 0!rom these lengths1 and changes to displaying the reads !or that( The re!erence se%uence !or the mapped reads can be changed manually in the drop do'n list in the toolbar at the top o! the 9amEie'(

3n the case 'hen the re!erence se%uences are concatenated together into one 0e(g( in a multiple -".T" se%uence1 and the se%uence length matches the sum o! se%uence lengths gi&en in the header o! the 9"7/ "rtemis 'ill try to match the names 0e(g( locusKtag or label1 o! the !eatures 0e(g( contig or chromosome1 against the re!erence se%uence names in the 9"7( 3t 'ill then adHust the read positions accordingly using the start position o! the !eature( 2hen open the 9amEie' can be con!igured &ia the popup menu 'hich is acti&ated by clicBing on the 9amEie' panel( The MEie'M menu allo's the reads to be displayed in a number o! &ie'sJ stacB/ strandstacB/ paired-stacB/ in!erred siIe and co&erage( 3n "rtemis the 9amEie' display can be used to calculate the number o! reads mapped to the regions co&ered by selected !eatures( 3n addition the reads per Bilobase per million mapped reads 0R,C71 &alues !or selected !eatures can be calculated on the !ly( $ote this calculation can taBe a 'hile to complete( Eariant Call -ormat 0EC-1 !iles can also be read( The EC- !iles need to be compressed and inde=ed using bgIip and tabi= respecti&ely 0see the tabi= manual and do'nload page1( The compressed !ile gets read in 0e(g( !ile(&c!(gI1 and belo' are the commands !or generating this !rom a EC- !ileJ
bg(ip file+"cf tabix -p "cf file+"cf+g(

"lternati&ely a 9inary EC- 09C-1 can be inde=ed 'ith 9C-tools and read into "rtemis or "CT( "s 'ith reading in multiple 9"7 !iles/ it is possible to read a number o! 0compressed and inde=ed1 EC!iles by listing their !ull paths in a single !ile( They then get displayed in separate ro's in the EC- panel(

-or single base changes the colour represents the base it is being changed to/ i(e( T blacB/ G blue/ " green/ C red( There are options a&ailable to !ilter the display by the di!!erent types o! &ariants( Right clicBing on the EC- panel 'ill display a pop-up menu in 'hich there is a M-ilter(((M menu( This opens a 'indo' 'ith

checB bo=es !or a number o! &araint types and properties that can be used to !ilter on( This can be used to sho' and hide synonymous/ non-synonymous/ deletion 0grey1/ insertion 0magenta1/ and multiple allele 0orange line 'ith a circle at the top1 &ariants( 3n this 'indo' there is a checB bo= to hide the &ariants that do not o&erlap C#. !eatures( There is an option to marB &ariants that introduce stop codons 0into the C#. !eatures1 'ith a circle in the middle o! the line that represents the &ariant( There are also options to !ilter the &ariants by &arious properties such as their %uality score 0D+"L1 or their depth across the samples 0#,1( ,lacing the mouse o&er a &ertical line sho's an o&er&ie' o! the &ariation as a tooltip( "lso right clicBing o&er a line then gi&es an e=tra option in the pop-up menu to sho' the details !or that &ariation in a separate 'indo'( There are also alternati&e colouring schemes( 3t is possible to colour the &ariants by 'hether they are synonymous or non-synonymous or by their %uality score 0the lo'er the %uality the more !aded the &ariant appears1( There is an option to pro&ide an o&er&ie' o! the &ariant types 0e(g( synonymous/ non-synonymous/ insertion/ deletion1 !or selected !eatures( "lso/ !iltered data can be e=ported in EC- !ormat/ or the reconstructed #$" se%uences o! &ariants can be e=ported in -".T" !ormat !or selected !eatures or regions !or !urther analyses( These se%uences can be used as input !or multiple se%uence alignment tools(

Sa$e 8efault 3ntry

.a&e the de!ault entry to the !ile it came !rom/ unless the entry has been gi&en a ne' name/ in 'hich case the entry is sa&ed to a !ile 'ith that name( 3! the entry has no name/ "rtemis 'ill prompt the user !or a ne' name( Pshortcut BeyJ .Q

Sa$e An 3ntry
This item 'ill do the same as A.a&e #e!ault 8ntryA !or the chosen entry(

Sa$e An 3ntry As
This sub-menu contains the less !re%uently used sa&e !unctions(

&e- .ile
"sB !or the name o! !ile to sa&e the gi&en entry to( The name o! entry 0as displayed in the entry button line1 'ill change to the ne' name(

3M4L .ormat
This does the same as A.a&e "n 8ntry "s -R $e' -ile (((A/ but 'ill 'rite the !eatures and se%uence o! the entry in 879L !ormat( $ote that currently the header o! a G8$9"$C entry canMt be con&erted to the

e%ui&alent 879L header 0it 'ill be discarded instead1(

!3&4A&6 .ormat
This does the same as A.a&e "n 8ntry "s -R $e' -ile (((A/ but 'ill 'rite the !eatures and se%uence o! the entry in G8$9"$C !ormat( $ote that currently the header o! a 879L entry canMt be con&erted to the e%ui&alent G8$9"$C header 0it 'ill be discarded instead1(

Se uin Table .ormat

This sa&es a !ile in .e%uin table !ormat 'hich is used by .e%uin(

!.. .ormat
2rites the !eatures in G-- !ormat and se%uence o! the entry in -".T" !ormat to a !ile selected by the user( $ote that i! you use this !unction on an 879L or G8$9"$C entry the header 'ill discarded(

3M4L Submission .ormat

This does the same as A.a&e "n 8ntry "s -R 879L -ormat (((A/ but 'ill 'rite an entry*tab !ile that contains only &alid 879L %uali!iers 0see the section called extra_qualifiers in Chapter 1 and &alid 879L Beys 0see the section called extra_keys in Chapter 1( 3t 'ill also checB that the start and stop codons o! each C#. are sensible/ that no t'o !eatures ha&e the same Bey and location and that all re%uired 879L %uali!iers are present(

Sa$e All 3ntries

This acts liBe A.a&e #e!ault 8ntryA/ but sa&e all the entries(

Write

Amino Acids ,f Selected .eatures

,rompt !or a !ile name and then 'rite the translation o! the bases o! the selected !eatures to that !ile( The !ile is 'ritten in -".T" !ormat(

/IR 8atabase ,f Selected .eatures

,rompt !or a !ile name and then 'rite the translation o! the bases o! the selected !eatures to that !ile( The !ile is 'ritten in ,3R !ormat 0similar to -".T"/ but 'ith a S as the last line o! each record1(

4ases ,f Selection
,rompt !or a !ile name and then 'rite the bases o! the selection to that !ile in the selected !ormat( 3! the selection consists o! !eatures 0rather than a base range1 then the bases o! each !eature 'ill be 'ritten to the !ile as a separate record( 3! the selection is a range o! bases/ then those bases 'ill be 'ritten(

%pstream 4ases ,f Selection

,rompt !or a number and a !ile name/ then 'rite that many bases upstream o! each selected !eature to the !ile in the selected !ormat( -or e=ample i! the selected !eature has a location o! A 100++200A/ then asBing !or :0 upstream 'ill 'rite the bases in the range :0 to 99( 2riting upstream bases o! a !eature on the complementary strand 'ill 'orB in the e=pected 'ay(

8o-nstream 4ases ,f Selection

,rompt !or a number and a !ile name/ then 'rite that many bases do'nstream o! each selected !eature to the !ile in the selected !ormat(

All 4ases
,rompt !or a !ile name/ then 'rite the complete se%uence to that !ile in the selected !ormat(

Codon %sa"e of Selected .eatures

,rompt !or a !ile name/ then 'rite a codon usage table !or the selected !eatures( The !ile in 'ritten in the same !ormat as the data at CaIusa codon usage database site( 3n the output !ile each codon is !ollo'ed by itMs occurrence count 0per thousand1 and itMs percentage occurrence( 0.ee the section called Add !sage 1lots ... to !ind out ho' to plot a usage graph1(

Clone This Windo7aBe a ne' main 'indo' 'ith the same contents as the current 'indo'( "ll changes in the old 'indo'

'ill be re!lected in the ne' 'indo'/ and &ice &ersa( The e=ception to this rule is the selection 0see the section called +he &election in Chapter 11/ 'hich is not shared bet'een the old and ne' 'indo'(

Sa$e As Ima"e .iles Ipn"(s$"J

,rint out the contents o! the current 'indo'( "ll or some o! the 'indo' panels can be selected !or printing to an image !ile( .EG 0scalable &ector graphics1 is an @7L based &ector image !ormat( These images can be con&erted to a raster image 0e(g( png/ ti!!1 at any resolution by e=porting it !rom applications such as 3nBscape 0httpJ**inBscape(org*1 or gimp 0httpJ**'''(gimp(org*1( Ther!ore the .EG !ormat can be use!ul !or creating publication %uality !igures( The other !ormats a&ailable 0png/ Hpeg etc1 and are raster or bitmap images(

/rint
This option can be used to print the contents o! the current 'indo' to a !ile as ,ost.cript or to a printer(

/rint /re$ieThis opens the print image in a pre&ie' 'indo'( This sho's 'hat the image 'ill looB liBe 'hen printed to a !ile(

/references
This enables the user to de!ine their o'n shortcut pre!erences(

Close
Close this 'indo'(

The 3ntries Menu

The items in this menu are used to change 'hich entry is the de!ault entry and 'hich entries are acti&e 0see the section called +he *Entry* in Chapter 11( "t the bottom o! the menu there is a toggle button !or each entry 'hich controls 'hether the entry is acti&e or not( These toggle buttons 'orB in a similar 'ay the the buttons on the entry button line 0see the section called +he Entry B tton $ine1(

4ere is a description o! the other menu itemsJ

Set &ame ,f 3ntry

.et the name o! an entry chosen !rom a sub-menu( The name o! the entry is used as the name o! the !ile 'hen the entry is sa&ed(

Set 8efault 3ntry

.et the de!ault entry by choosing one o! the entries !rom the sub-menu( 0.ee the section called +he Defa lt Entry in Chapter 11(

Remo$e An 3ntry
Remo&e an entry !rom "rtemis by choosing one o! the entries !rom the sub-menu( The original !ile that this entry came !rom 0i! any1 'ill not be remo&ed(

Remo$e Acti$e 3ntries

Remo&e the entries that are currently acti&e( 0.ee the section called +he Acti2e Entries in Chapter 11(

8eacti$ate All 3ntries

Choosing this menu item 'ill deacti&ate all entries( 0.ee the section called +he Acti2e Entries in Chapter 1(1

The Select Menu

The items in this menu are used to modi!y the current selection 0see the section called +he &election in Chapter 11( "rtemis sho's a short summary o! the current selection at the top o! the main 'indo' 0see 2 !or details1((

.eature Selector ...

5pen a ne' -eature .elector 'indo'( This 'indo' allo's the user to choose 'hich !eatures to select or

&ie' based on !eature Beys 0see the section called E-B$#Genban) ,eat re .eys in Chapter 11/ %uali!ier &alues 0see the section called E-B$#Genban) ,eat re / alifiers in Chapter 11 and amino acid moti!s( The .elect button 'ill set the selection to the contain those !eatures that match the gi&en Bey/ %uali!ier and amino acid moti! combination( The Eie' button 'ill create a ne' !eature list 0see the section called +he ,eat re $ist1 containing only those !eatures that match the gi&en Bey/ %uali!ier and amino acid moti! combination(

All
Reset the selection so that nothing is selected then select all the !eatures in the acti&e entries( Pshortcut BeyJ "Q

All 4ases
Reset the selection so that nothing is selected then select all the bases in the se%uence(

Select All .eatures in &on0matchin" Re"ions

.elect all !eatures that ha&e no corresponding match in "CT( This is used to higlight regions that are di!!erent bet'een sets o! se%uence( 3t 'ill only taBe into account matches that ha&e not been !iltered out using the score/ identity or length cut-o!!(

&one
Clear the selection so that nothing is selected( Pshortcut BeyJ $Q

4y 6ey
"sB the user !or a !eature Bey/ reset the selection so that nothing is selected/ then select all the !eatures 'ith the Bey gi&en by the user(

C8S .eatures
Reset the selection so that nothing is selected/ then select all the C#. !eatures that do not ha&e a *pseudo %uali!ier(

Same 6ey
.elect all the !eatures that ha&e the same Bey as any o! the currently selected !eatures(

,pen Readin" .rame

8=tend the current selection o! bases to co&er complete open reading !rames( .electing a single base or codon and then choosing this menu item has a similar e!!ect to double clicBing the middle button on a base or residue 0see the section called Changing the &election from a 0ie( 'indo( !or details1(

.eatures ,$erlappin" Selection

.elect those 0and only those1 !eatures that o&erlap the currently selected range o! bases or any o! the currently selected !eatures( The current selection 'ill be discarded(

.eatures Within Selection

.elect those 0and only those1 !eatures that are !ully contained by the currently selected range o! bases or any o! the currently selected !eatures( The current selection 'ill be discarded(

4ase Ran"e ...

"sB the user !or a range o! bases/ then select those bases( The range should looB something liBe thisJ 100-200/ complement,100++2003/ 100+200 or 100++200( 3! the !irst number is larger than the second the bases 'ill be selected on the !or'ard strand/ other'ise they 'ill be selected on the re&erse strand 0unless there is a complement around the range/ in 'hich case the sense is re&ersed1(

.eature AA Ran"e ...

"sB the user !or a range o! amino acids in the selected !eature and select those bases( The range should looB something liBe thisJ 100-200/ or 100++200(

To""le Selection
3n&ert the selection - a!ter choosing this menu item the selection 'ill contain only those !eatures that 'ere not in the selection be!orehand(

The Hie- Menu

Selected .eatures
5pen a &ie' 'indo' !or each selected !eature sho'ing itMs !eature table entry( Pshortcut BeyJ EQ

Selection
5pen a &ie' 'indo' that 'ill sho' the current selection( The 'indo' is updated as the selection changes/ so it can be le!t open( 2hen one !eature is selected the 'indo' 'ill sho' the te=t 0879L/ Gen9anB or G-- !ormat1 o! the !eature/ the base composition/ GC percentage/ correlation score 0see the section called Correlation

&cores1/ and the bases and translation o! the se%uence o! the !eature( 2hen t'o or more !eatures are selected the 'indo' 'ill sho' the te=t 0879L/ Gen9anB or G-- !ormat1 o! the !eatures/ the base composition/ a&erage GC percentage/ a&erage correlation score/ minimum*ma=imum GC content and minimum*ma=imum correlation score o! the !eature se%uence( 2hen a range o! bases is selected the 'indo' 'ill sho' the base composition/ GC content percentage and the bases and translation o! the se%uence o! the !eature(

Search Results
5n this sub-menu allo's the user to &ie' the results o! !eature searches that are launched !rom the run menu in "rtemis 0see the section called +he R n -en 1(

C8S !enes And /roducts

,op up a !eature list 0see the section called +he ,eat re $ist1 o! the C#. sho'ing the gene names 0!rom the *gene %uali!ier1 and the product 0!rom the *product %uali!ier1( This list includes pseudo genes(

.eature .ilters
8ach o! the items in this sub-menu each allo' the user to &ie' a subset o! the acti&e !eatures( "n e=ample o! a subset is all those !eatures 'ith misc_feature as a Bey( The !eatures are displayed in a ne' 'indo' that contains a menu bar 'ith possible actions to apply to the subset/ and !eature list 0see the section called +he ,eat re $ist1( 7ost o! the possible actions 'ill apply only to the !eatures in the list( -or e=ample A.ho' 5&er&ie'A in the Eie' menu 0see the section called O2er2ie(1 'ill include statistics only on the !eatures in the list(

Suspicious Start Codons ...

.ho' those C#. !eatures that ha&e a suspicious start codon( ie( the !irst codon o! the !eature isnMt "TG 0in euBaroytic mode1 or "TG/ GTG and TTG 0in proBaryotic mode1( This !unction is e!!ected by the setting o! the A8uBaroytic 7odeA option in the main options menu 0see the section called Genetic Code +ables in Chapter 2 !or more1(

Suspicious Stop Codons ...

.ho' those C#. !eatures that ha&e a suspicious stop codon( ie( the last codon o! the !eature isnMt one o! T""/ T"G or TG"(

&on 3M4L 6eys ...

.ho' those !eatures that ha&e a Bey that isnMt &alid !or 879L*Gen9anB entries(

8uplicated .eatures ...

.ho' those !eatures that are duplicated 0ie( !eatures that ha&e the same Bey and location as another !eature1( These sort o! duplicates arenMt allo'ed by the 879L database(

,$erlappin" C8S .eatures ...

.ho' those C#. !eatures that o&erlap another C#. !eature 0on either strand1(

.eatures Missin" Re uired 7ualifiers ...

.ho' those !eatures that are missing a %uali!ier that is re%uired by the 879L database(

.ilter 4y 6ey ...

.ho' those !eatures that ha&e a Bey chosen by the user(

Selected .eatures ...

.ho' the currently selected !eatures in a ne' !eature list( The contents o! the list 'ill remain the same e&en i! selection subse%uently changes( This is use!ul !or booBmarBing a collection o! !eatures !or later use(

,$er$ie5pen a ne' 'indo' the 'ill sho' a summary o! the acti&e entries and some statistics about the se%uence 0such as the GC content1( Pshortcut BeyJ 5Q

Se uence Statistics
The o&er&ie' 'indo' sho' the !ollo'ing statistics about the se%uenceJ $umber o! bases(

 GC percentage( The number o! each nucleotide in the se%uence( GC percentage o! non-ambiguous bases - ie( the GC content percentage ignoring bases other than "/T/C and G( This should be the same as the AGC percentageA abo&e(

.eature Statistics
The o&er&ie' 'indo' also sho's the !ollo'ing statistics about the !eatures in the acti&e entries 0i! there are any !eatures1( $ote that the AgenesA are the non-pseudo C#. !eatures( $umber o! !eatures in the acti&e entries 0see the section called +he Acti2e Entries in Chapter 11( Gene density - the a&erage number o! non-pseudo C#. !eatures per 1000 bases( "&erage gene length - the a&erage length o! non-pseudo C#. !eatures 0not including introns1( $umber o! non-spliced genes( $umber o! spliced genes( $umber o! pseudo genes 0ie( C#. !eatures 'ith a *pseudo %uali!ier1( ,rotein coding 0C#.1 !eatures( ,rotein coding 0C#.1 bases( ,rotein coding percentage - ie( the number o! coding bases e=cluding introns( Coding percentage 0including introns1( " summary o! the number o! !eatures o! each Bey 0type1 and their colours(

.or-ard Strand ,$er$ie5pen a ne' 'indo' the 'ill sho' a summary o! the !eatures and bases o! the !or'ard strand(

Re$erse Strand ,$er$ie5pen a ne' 'indo' the 'ill sho' a summary o! the !eatures and bases o! the re&erse strand(

.eature 4ases
Create a &ie' 'indo' !or each selected !eature/ 'hich sho's bases o! the !eature(

.eature 4ases As .ASTA

Create a &ie' 'indo' !or each selected !eature/ 'hich sho's bases o! the !eature in -".T" !ormat(

.eature Amino Acids

Create a &ie' 'indo' !or each selected !eature/ 'hich sho's amino acids o! the !eature(

.eature Amino Acids As .ASTA

Create a &ie' 'indo' !or each selected !eature/ 'hich sho's amino acids o! the !eature in -".T" !ormat(

.eature Statistics
.ho' some statistics about each selected !eature( 5n the le!t on the !eature in!ormation 'indo' is the amino acid composition o! the !eature( 5n the right is the codon composition o! the !eature(

.eature /lots
5pen a 'indo' !or each selected !eature that sho's a plot o! the Cyte-#oolittle 4ydrophobicity Pshort nameJ h'drophobicit'Q/ the 4opp-2oods 4ydrophilicity Pshort nameJ h'drophilicit'Q/ and an appro=imation o! the GCG Coiled Coils algorithm Pshort nameJ coiled_coilQ( 0-or more detail about the coiled coils algorithm see A,redicting Coiled Coils !rom ,rotein .e%uencesA/ .cience Eol( 2:2 page 11 2(1 Pshortcut BeyJ 2Q .ome general in!ormation about graphs and plots in "rtemis can be !ound in the section called Graphs and 1lots( Con!iguration options !or graphs are described in the section called Options ,or 1lots and Graphs in Chapter (

The !oto Menu

The items in this menu allo' the user to na&igate around the se%uence and !eatures(

&a$i"ator ...
5pen a ne' na&igation 'indo'( Pshortcut BeyJ GQ This 'indo' allo's the user to per!orm !i&e di!!erent tasBsJ 1( Scroll all the $ie-s so that a particular base is in the centre of the display . To use this !unction/ type a base position into the bo= to the right o! the AGoto 9aseJA label then press the goto button at the bottom o! the 'indo'( The re%uested base 'ill be selected and then the o&er&ie' display and the #$" display 'ill scroll so that the base is as near as possible to the middle o! the main 'indo'( 2( .ind the ne)t feature that has the "i$en "ene name . To use this !unction/ type a gene name into the bo= to the right o! the AGoto -eature 2ith This Gene $ameJA label and then press the goto button( "rtemis 'ill select the !irst !eature 'ith the gi&en te=t in any o! itMs %uali!iers and 'ill then scroll the display so that !eature is in &ie'( ;( .ind the ne)t feature that has a ualifier containin" a particular strin" . To use this !unction/ type a string into the bo= to the right o! the AGoto -eature 2ith This Duali!ier EalueJA label and then press the goto button( "rtemis 'ill select the !irst !eature 'ith the gi&en string in any o! itMs %uali!ier &alues 0see the section called E-B$#Genban) ,eat re / alifiers in Chapter 11 and 'ill then scroll the display so that !eature is in &ie'( 4( .ind the ne)t feature that has a particular 5ey . To use this !unction/ type a Bey into the bo= to the right o! the AGoto -eature 2ith This CeyJA label and then press the goto button( "rtemis 'ill select the !irst !eature 'ith the gi&en Bey and 'ill then scroll the display so that !eature is in &ie'( :( .ind the ne)t occurrence of a particular base pattern in the se uence . To use this !unction/ type a base pattern into the bo= to the right o! the A-ind 9ase ,atternJA label and then press the goto button( "rtemis 'ill select the !irst contiguous group o! bases on either strand that match the gi&en base pattern and 'ill then scroll the display so that those bases are in &ie'( "ny 3+9 base code can be used in the pattern/ so !or e=ample searching !or aanntt 'ill match any si= bases that start 'ith AaaA and ends 'ith AttA( .ee Table ;-1 !or a list o! the a&ailable base codes( ( .ind the ne)t occurrence of a particular residue pattern in the se uence . To use this !unction/ type a amino acid pattern into the bo= to the right o! the AGoto "mino "cid .tringJA label and then press the goto button( "rtemis 'ill select the !irst contiguous group o! bases on either strand that translate to the gi&en amino acids and 'ill then scroll the display so that those bases are in &ie'( The letter M@M can be used as an ambiguity code/ hence M""@@@##M 'ill match M""LRT##M or M""TTT##M etc( $ote that !or all the !unctions abo&e e=cept the !irst 0AGoto 9aseA1/ i! the A.tart search at beginningA option is set or i! there is nothing selected the search 'ill start at the beginning o! the se%uence( 5ther'ise the search 'ill start at the selected base or !eature( This means that the user can step through the matching bases or !eatures by pressing the goto button repeatedly( 3! the A3gnore CaseA toggle is on 0'hich is the de!ault1 "rtemis 'ill ignore the di!!erence bet'een upper and lo'er case letters 'hen searching !or a gene name/ a %uali!ier &alue or a !eature Bey( The A"llo' .ubstring 7atchesA toggle a!!ects 2 and ;( 3! on "rtemis 'ill search !or %uali!ier &alues that contain the gi&en characters( -or e=ample searching !or the genename C#C 'ill !ind C#C1/ C#C2/ "9C#C etc( 3! the toggle is o!! "rtemis 'ill only !ind e=act matches/ so searching !or the gene C#C 'ill only !ind !eatures that ha&e %gene=# D # not %gene=# D 11#(

Start of Selection
.croll all the &ie's so that the !irst base o! the selection is as close to the centre as possible( 3! the a range o! bases is selected the &ie's 'ill mo&e to the !irst base o! the range( 3! one or more !eatures are selected/ then the !irst base o! the !irst selected !eature 'ill be centred( 5ther'ise/ i! one or more segments 0see the section called ,eat re &egments in Chapter 11 is selected then the !irst base o! the !irst selected segment 'ill be centred( Pshortcut BeyJ control-le!tQ

3nd of Selection
This does the same as AGoto .tart o! .electionA/ but uses the last base o! the selected range or the last base o! the last selected !eature or segment( Pshortcut BeyJ control-rightQ

.eature Start
.croll the &ie's to the start o! the !irst selected !eature(

.eature 3nd
.croll the &ie's to the end o! the !irst selected !eature(

Start of Se uence
.croll the &ie's so that the start o! the se%uence is &isible( Pshortcut BeyJ control-upQ

3nd of Se uence
.croll the &ie's so that the end o! the se%uence is &isible( Pshortcut BeyJ control-do'nQ

.eature 4ase /osition ...

"sB the user !or a base position 'ithin the !irst selected !eature/ then scroll the &ie's so that that base position is centred(

.eature Amino Acid ...

"sB the user !or an amino acid position 'ithin the !irst selected !eature/ then scroll the &ie's so that that position is centred(

The 3dit Menu

This menu contains most o! the !unctions that change the entries( $ote that the changes 'ill not be sa&ed bacB to the original !iles until one o! the sa&e !unctions in the -ile menu is used 0see the section called &a2e An Entry1(

%ndo
This !unction 'ill undo the last change that 'as made using the 8dit or Create menus( +p to 20 changes can be undone( This menu item is only enabled 'hen there is something to undo( This limit can be changed in the options !ile 0see the section called undo_levels in Chapter 1( Pshortcut BeyJ +Q

Redo
This !unction 'ill redo the last undo operation(

Selected .eatures in 3ditor

5pen an edit 'indo' !or each selected !eature( Pshortcut BeyJ 8Q

-rom the top do'n the edit 'indo' has these partsJ

1( "t the top le!t is a selector !or choosing the Bey o! the !eature( This only contains a subset o! the legal Beys( The subset can be changed by changing the common_ke's option in the options !ile 0see the section called common_keys in Chapter 1( "t the top right o! the edit 'indo' is a selector !or adding a %uali!ier( -or e=ample choosing note !rom the menu 'ill insert %note=## into the %uali!ier edit area( 2( ?ust belo' the Bey and %uali!ier selector is the location entry !ield( "rtemis understands most o! the 879L location synta=/ including Hoins/ complements/ ranges 'ith non-e=act ends 0eg( ,100+2003++4F801 and re!erences to other entries 0eg( Moin,100++20015@A2F>1$100++20031( ;( 9elo' the location is a ro' o! buttonsJ The omplement button 'ill complement the contents o! the location !ield( The 9rab =ange button 'ill grab the currently selected range into the location !ield( The =emo"e =ange button 'ill remo&e the selected bases !rom the location string( This is normally used to create an intron in a !eature( ,ressing the 9oto Feature button has the same e!!ect as the A.tart o! .electionA item in the AGotoA menu( 0.ee the section called &tart of &election !or more1( The ;ser Pualifiers button opens a tool !or maintaining user de!ined lists o! %uali!iers 0i(e( %uali!iers in the !orm tag O &alue pairs on separate lines1 and the option to read %uali!iers !rom 595 !ormatted !iles or +RLs( 3n the intial screen 0see belo'1 you are in&ited to import your %uali!ier list !rom the import options in the A-ileA menu( These lists can be optionally sa&ed bet'een sessions in the !ile M(artemis(%uali!iersM in the home directory(

2hen a %uali!ier list or 595 !ile has been added then it is possible to search !or Bey'ords 'ithin a list( The %uali!er selected in the drop do'n list 0under the .8"RC4 button1 can then be added to the current !eature annotation or added to selected !eatures in "rtemis( 3! the Bey'ords te=t !ield is le!t blanB then all %uali!iers are a&ailable !rom the drop do'n list o! %uali!ier &alues(

4( The centre o! the edit 'indo' contains the %uali!ier entry section( The %uali!iers should be entered the in same 'ay the appear in the !eature table part o! an 879L entry/ but 'ithout the leading FT and spaces( :( The bottom o! the 'indo' contains three buttons( The KO button 'ill update the !eature 'ith the changes that ha&e been made by the user and 'ill then close the edit 'indo'( The ancel button 'ill discard the changes and then close the 'indo'( The >ppl' 'ill maBe the changes/ but 'ill not close the 'indo'( 9e!ore any changes are made the location and the %uali!iers are checBed !or !ormatting errors( "ny errors 'ill brought to the attention o! the user through the use o! annoying pop-up bo=es( $o changes 'ill be per!ormed until there all errors ha&e been !i=ed(

Subse uence Iand .eaturesJ

7aBe a copy 0in a ne' edit 'indo'1 o! the selected bases and the !eatures in that range( "ny !eatures that o&erlap the end o! the range 'ill be truncated(

.ind ,r Replace 7ualifier Te)t

This opens a search 'indo' 'ith options to !ind or replace %uali!ier te=t( The search can be restricted to !eatures 'ith a gi&en Bey and*or it can be restricted to a gi&en %uali!ier name( 9oolean operators 0and*or1 can be used in the search( ClicBing on the 5ho! Aoolean 5earch Kptions displays 4 options( 1( The ;se boolean operators ,and1 or1 R 03 means that it uses any o! these operators that are in the Find te=t !ield( 2( The 6atch an' string ,i+e+ x K= '3 means that the 'ords in the Find te=t !ield 'ill be separated by an 5R condition( .o that it !inds those !eatures 'ith %ulai!iers that contain any o! the 'ords( ;( The 6atch all string ,i+e+ x >:D '3 means that the 'ords in the Find te=t !ield 'ill be separated by an "$# condition( .o that it !inds those !eatures 'ith %ulai!iers that contain all o! the 'ords( 4( The :o boolean search option is the de!ault( This means it searches !or those !eatures 'ith

%uali!iers that contain the complete te=t !rom the Find te=t !ield( 3n addition selecting the #uplicate Duali!iers tab pro&ides options to search !or or delete duplicate %uali!iers(

7ualifierIsJ of Selected .eature

Chan"e ...
This !unction allo's the user to add or change %uali!iers on all the selected !eatures in one operation( The main part o! the 'indo' acts liBe the %uali!ier editing !ield o! the !eature edit 'indo' 0see the section called &elected ,eat res in Editor 1(

Remo$e ...
This !unction allo's the user to remo&e all %uali!iers 'ith a particular name !rom all the selected !eatures(

Con$ert ...
This !unction allo's the user to con&ert all %uali!iers o! a particular type to another %uali!ier !or all the selected !eatures(

Selected .eatureIsJ
8uplicate
7aBe a copy o! each selected !eature( 8ach ne' !eature 'ill be added Hust a!ter the original in the same entry as the original( Pshortcut BeyJ #Q

Mer"e
Create a ne' !eature that contains all the e=ons and %uali!iers o! the selected !eatures( The selected !eatures must all ha&e the same Bey( Pshortcut BeyJ 7Q

%nmer"e
3! the selection contains e=actly t'o e=ons and those e=ons are adHacent in the same !eature/ split the

!eature into t'o pieces bet'een the e=ons( The original !eature is truncated and a ne' !eature is created( The %uali!iers o! the old !eature are copied to ne' !eature(

%nmer"e All Se"ments

"ll e=ons in a !eature are unmerged(

8elete
Remo&e each selected !eature !rom itMs entry( Pshortcut BeyJ control-deleteQ

8elete 3)ons
#elete the selected e=ons( The last e=on o! a !eature canMt be deleted 0delete the 'hole !eature instead1(

Remo$e Introns
#elete the selected introns(

Mo$e Selected .eatures To

7o&e the selected !eatures to another entry( Choose the destination entry !rom the sub-menu(

Copy Selected .eatures To

Copy the selected !eatures to another entry( Choose the destination entry !rom the sub-menu(

Trim Selected .eatures

To Met
-or each o! the selected !eatures this !unction 'ill attempt to mo&e the start position to the !irst "TG in the !eature i! the !eature does not already start on a "TG codon( 3! there is no "TG in the !irst thirty percent o! the bases o! the !eature the start position 'ill be unchanged( The search 'ill stop at the end o! the !irst segment o! a multi-segment !eature(

To Any
This 'orBs in the same 'ay as ATrim .elected -eatures To 7etA/ but 'ill attempt to mo&e the start position o! the !eature to the !irst TTG/ "TG or GTG in the !eature i! it does not already start on one o! those codons( "s abo&e it 'ill only search the !irst thirty percent o! the !eature bases and 'ill only search the !irst segment o! a multi-segment !eature(

To &e)t Met
-or each o! the selected !eatures this !unction 'ill attempt to mo&e the start position to the ne=t "TG in the !eature 0the !irst codon is sBipped1( 3! there is no "TG in the !irst thirty percent o! the bases o! the !eature the start position 'ill be unchanged( The search 'ill stop at the end o! the !irst segment o! a multisegment !eature( Pshortcut BeyJ TQ

To &e)t Any
This 'orBs in the same 'ay as ATrim .elected -eatures To $e=t 7etA/ but 'ill attempt to mo&e the start position o! the !eature to the ne=t TTG/ "TG or GTG in the !eature 0the !irst codon is sBipped1( "s abo&e it 'ill only search the !irst thirty percent o! the !eature bases and 'ill only search the !irst segment o! a multi-segment !eature( Pshortcut BeyJ 6Q

3)tend Selected .eatures

To /re$ious Stop Codon
8=tend each o! the selected !eatures 'hich do not start on a stop codon so that each !eature starts Hust a!ter the pre&ious stop codon in this reading !rame( Pshortcut BeyJ DQ

To &e)t Stop Codon

8=tend each o! the selected !eatures 'hich do not end on a stop codon so that each !eature ends Hust be!ore the ne=t stop codon in this reading !rame(

To &e)t Stop Codon and .i)

.ame as abo&e but in addition this !i=es the stop codons(

.i) Stop Codons

ChecB and !i= the stop codons to all the selected !eatures( -or each !eature i! the last codon is a stop codon/ then all is 'ell/ nothing !urther is done to the !eature( 3! the last codon is not a stop codon/ but the &ery ne=t codon is a stop codon/ then the end o! the !eature is mo&ed !or'ard by three bases( 3! both the last codon and the &ery ne=t codon a!ter the !eature are not stop codons/ the !eature is selected/ an error message is displayed and processing stops immediately(

Automatically Create !ene &ames

"sB !or a gene name pre!i= 0using a te=t re%uester1/ and then gi&e a uni%ue gene name to each C#. !eature in the acti&e entries using that pre!i=( -or e=ample i! there are !our C#. !eatures 'ith locationsJ A1++800A/ Acomplement,100++N003A/ A200++G00A and Acomplement,F00++E003A/ entering 5@A 1N>F 'ill gi&e the !our !eatures these namesJ 5@A 1N>F+01/ 5@A 1N>F+02c/ 5@A 1N>F+0F and 5@A 1N>F+02c(

.i) !ene &ames

-or each selected C#./ add the gene name !rom the C#. to neighbouring*o&erlapping mR$"/ intron/ e=on/ gene/ :M+TR and ;M+TR !eatures( 2arn about inconsistencies such as o&erlapping C#.s(

4ases
Re$erse And Complement
Re&erse and complement the se%uence and all the !eatures in all the entries 0acti&e and inacti&e1(

Re$erse And Complement Selected Conti"

Re&erse and complement the se%uence and all the !eatures in a selected contig !eature( 3! this option is used in "CT then all the matches 'ithin the contig are also re&ersed( "ny matches e=tending past the boundary o! the contig are deleted( The changes to the comparison !ile can be sa&ed by right clicBing in the comparison 'indo' and selecting A.a&e Comparison -ile(((A( 4o'e&er/ ideally the comparison bet'een the t'o se%uences should be recalculated(

8elete Selected 4ases

#eletes the selected range o! bases 0i! any1 !rom both strands( The deletion 'ill not proceed i! the selected range o&erlaps any !eatures(

Add 4ases At Selection

,rompt the user !or some bases to insert Hust be!ore the selected bases( The operation 'ill not proceed i! there is no selected range/ but bases can be inserted any'here in the se%uence/ including inside a !eature( The same bases/ re&ersed and complemented/ 'ill be inserted at the corresponding place on the opposite strand(

Add 4ases .rom .ile ...

,rompt the user !or the name o! a !ile containing the bases to insert Hust be!ore the selected bases(

Replace 4ases At Selection

,rompt the user !or some bases to replace the selected bases(

Conti" Reorderin" ...

5pens a MContig ToolM displaying contigs/ i(e( 'ith !eature Beys M!astaKrecordM or McontigM( The !ormer being created automatically !or each se%uence 'hen a mutiple !asta se%uence !ile is read in( The contigs in this tool can then indi&idually be selected and dragged and dropped to another location( 3n this 'ay the order o! contigs and !eatures 'ithin a contig can be changed( 3! this is used in "CT then the matches are also reordered 'ith respect to the change in the se%uence( 3! a match spans the boundary o! a contig that is being mo&ed then i! possible it is split( 3n some situations 'here there is a match 'ith MindelsM then this is not possible and the match is deleted( The changes to the comparison !ile can be sa&ed by right clicBing in the comparison 'indo' and selecting A.a&e Comparison -ile(((A( 4o'e&er/ ideally the comparison bet'een the t'o se%uences should be recalculated(

Geader ,f 8efault 3ntry

5pen a edit 'indo' containing the header o! the de!ault entry( Changes made in the edit 'indo' 'ill be applied immediately to the entry pro&ided there are no errors in the !ormatting o! the header(

The Create Menu

This menu contains !unctions !or creating ne' !eatures 0see the section called E-B$#Genban) ,eat res in Chapter 11 or entries 0see the section called +he *Entry* in Chapter 11(

&e- .eature
Create a ne' !eature in the de!ault entry 'ith a Bey o! AmiscK!eatureA 0see the section called E-B$#Genban) ,eat re .eys in Chapter 11/ a location o! that spans the 'hole se%uence and 'hich has no %uali!iers 0see the section called E-B$#Genban) ,eat re / alifiers in Chapter 11(

.eature .rom 4ase Ran"e

Create a ne' !eature in the de!ault entry 'ith a Bey o! AmiscK!eatureA/ no %uali!iers and a location that e=actly matches the selected range o! bases( 3! no bases are selected an error 'ill be reported( Pshortcut BeyJ CQ

Inter"enic .eatures
Create ne' !eatures bet'een C#. !eatures in the de!ault entry all 'ith the AmiscK!eatureA Bey(

.eatures .rom &on0matchin" Re"ions

Create !eatures in "CT spanning all the regions 'here a match is not to be !ound(

&e- 3ntry
Create a ne' entry 'ith no name and no !eatures( The ne' entry 'ill become the de!ault entry 0see the section called +he Defa lt Entry in Chapter 11(

Mar5 ,pen Readin" .rames ...

Create a !eature !or each AlargeA open reading !rame in the se%uence( The de!ault minimum siIe o! a AlargeA open reading !rame can be changed by changing the minimum_orf_si(e option 0see the section called minimum_orf_size in Chapter 1( 3! a codon usage !ile 0see the section called Add !sage 1lots ...1 has been read each ne' 5R- 'ill ha&e a codon usage score added as a *score %uali!ier( The ne' !eatures can then be !iltered !rom the display 0see A.et .core Cuto!!s (((A in the section called +he 1op- p -en 1(

Mar5 3mpty ,R.s ...

Create a !eature !or each open reading !rame that doesnMt already contain a !eature(

Mar5 ,pen Readin" .rames In Ran"e ...

Create a !eature !or each AlargeA open reading !rame in a range o! bases( " range must be selected be!ore using this command(

Mar5 .rom /attern ...

5pen a te=t re%uester to asB the user !or a base pattern/ then create a !eature !or each group o! bases that matches that pattern( " ne' entry 'ill be created to hold the !eatures 'ith the name AmatchesJ TpatternRA/ 'here TpatternR is the pattern that 'as entered be the user( "ny 3+9 base code can be used in the pattern/ so !or e=ample/ aanntt 'ill match any si= bases that start 'ith AaaA and ends 'ith AttA( Table @01. I%4 4ase Codes R O " or G 6 O C or T C O G or T 7 O " or C . O G or C 2 O " or T 9 O C/ G or T # O "/ G or T

$ O "/ C/ G or T 4 O "/ C or T E O "/ C or G

Mar5 Ambi"uities
Create a ne' !eature !or each blocB o! ambiguous bases( The ne' !eatures 'ill ha&e a Bey o! misc_feature and 'ill created in a ne' entry called Aambiguous basesA(

The Run Menu

This menu is primarily used !or running e=ternal programs on +$3@( "dditionally there are menu options to send se%uences !rom selected !eatures to the $C93 'eb 9L".T/ ,!am and R!am( 5nce con!igured correctly/ running an e=ternal program should be as simple as selecting some !eatures o! interest/ then choosing one o! the items !rom the run menu( 2hen the e=ternal programs !inishes the results can &ie'ed using the A.earch ResultsA item in the Eie' menu 0see the section called &earch Res lts1(

Confi"urin" the Run Menu

To use this !eature the run_blastp/ run_fasta etc( scripts that are supplied 'ith "rtemis 'ill need to be changed to re!lect the paths and databases that are con!igured at each site( $ote that the run scripts are stored in the etc% directory( 8ach e=ternal program that is listed in the options !ile 0see the section called feature_dna_programs in Chapter and the section called feature_protein_programs in Chapter 1 gets a ArunA menu item and a Aset optionsA menu item( -or each e=ternal program 0such as blastp1 there must be a shell script a&ailable that sets any necessary en&ironment &ariables and then launches the search*analysis program 0!or blastp the script is called run_blastp1( TaBing blastp as an e=ample/ this is the se%uence o! e&ents that occurs 'hen the user selects the ARun blastp on selected !eaturesA menu itemJ 1( "rtemis creates a ne' directory in the current directory called blastp( 2( " protein -".T" se%uence !ile is 'ritten in the ne' directory !or each selected !eature( 0-or a #$" search program such as blastn the !ile 'ill be a #$" -".T" !ile1( The se%uence !ile name 'ill be something liBeJ blastp%features+tab+se)+00001( ;( The name o! the e=pected output !ile is stored in the !eature in a %uali!ier called %blastp_file( 3! the entry is called features+tab then the %uali!ier 'ill be set to something liBeJ %blastp_file=#blastp%features+tab+se)+00001+out#( $ote that because the !ile name is stored in the entry you 'ill need to sa&e the entry to Beep the association bet'een the !eatures and the output !iles( 4( " !ile is then 'ritten 0called something liBe blastp%file_of_filenames+11 that contains the names o! all the ne'ly created se%uence !iles in the blastp directory( :( "rtemis then tries to read the run_blastp script !rom the "rtemis installation directory( The script is e=ecuted liBe thisJ run_blastp blastp%file_of_filenames+1 SoptionsT 'here SoptionsT currently must be a single 'ord 0normally a database to search1( 3n the case o! blastp*blastn*!asta etc( the second argument o! the script is passed directly to the blast*!asta as the database name( -or testing purposes it is possible to run run_blastp on the command line 'ith the same arguments as abo&e( run_blastp 'ill run blastp on each o! the se%uence !iles listed in

file_of_filenames+blastp and sa&e the output in the corresponding +out !ile( ( 3! the program is success!ully started/ control 'ill immediately return to the user( 2hen run_blastp !inishes a message 'ill be displayed to alert the user( 3! necessary/ it is possible to e=it once "rtemis indicates that the e=ternal program has been started and the entry has been sa&ed( run_blastp 'ill Beep running in the bacBground(

The !raph Menu

.ome general in!ormation about the graphs can be !ound in the section called Graphs and 1lots( Con!iguration options !or graphs are described in the section called Options ,or 1lots and Graphs in Chapter (

Gide All !raphs

This item 'ill turn o!! all the &isible graphs(

Add %sa"e /lots ...

This menu item prompts the user !or the name o! a !ile 'hich should contain codon usage data in the same !ormat as the data at this 'eb site( 3! "rtemis success!ully loads the codon usage !ile t'o ne' plots 'ill be added to the display menu and 'ill be immediately &isible( 5ne plot sho's the codon scores 0in a sliding 'indo'1 !or each o! the !or'ard reading !rames and the other sho's the same thing !or the re&erse reading !rames( Pshort nameJ codon_usageQ The graph is calculated using the codon pre!erence statistic !rom GribsBo& et al( 0$ucl( "cids Res( 12) :;9-:49 019U411( 4ere is an e=ample usage !ileJ
;;; ;; ;;> ;;9 F2+2, 1F+0, 2N+0, 22+0, 2E22F3 1D81D3 FD1FE3 FN1F23 ; ; F0+8, 28D1F3 ; 12+1, 1E12D3 ; > 1G+D, 2NE803 ; 9 E+0, 120883 ; 21+D, F2DN23 E+2, 12N1D3 > 12+G, 1D0G83 9 2+N, ND103 > ; 22+D, F221D3 > 10+D, 1NFGE3 > > 1F+D, 20EDE3 > 9 N+8, DG223 9 ; F0+2, 28FDG3 9 11+N, 1G81E3 9 > 18+G, 2FN2D3 9 9 8+F, E0113 ;>; 21+E, F2E2D3 ;> 11+E, 1GG213 ;>> 1+F, 1D223 ;>9 0+8, G083 >; 1N+F, 228GG3 > N+2, DN8F3 >> 2G+F, 210NN3 >9 10+D, 1N28G3 >>; >> >>> >>9 9>; 9> 9>> 9>9 FF+D, 1G+D, FD+F, 28+2, FE+1, 18+E, 22+F, 21+F, 8100D3 2NED83 8D0GD3 FGE283 8G2203 2FG2D3 NN8803 F1DGD3 ;9; E+D, 1FFG13 ;9 8+N, EFG23 ;9> 0+8, GFF3 ;99 10+D, 1NFN23 9; 1N+F, 222D83 9 N+2, DF1N3 9> G+D, 11EDN3 99 F+0, 22EG3 >9; 12+G, 2210E3 >9 D+2, 1FD083 >9> 11+1, 1NG223 >99 8+1, GN183 99; 22+0, FF1013 99 E+8, 12G1G3 99> 18+G, 2FN2F3 999 2+F, N2DG3

;; 28+F, FE0183 ; G+F, 10D223 ;> E+N, 12D8G3 ;9 N+F, D80F3 >;; >; >;> >;9 F8+0, 12+N, 1F+1, 20+D, 82NFN3 1D0003 1DG2N3 F1FGN3

9;; 2D+F, 220183 9; 11+0, 1N2DG3 9;> 12+F, 1E2813 9;9 E+F, 122223

Add %ser /lot ...

"rtemis is able to display some types o! user data in a graph that looBs liBe the GC content graph 0see the section called GC Content 4561( This menu item 'ill prompt the user !or the name o! a data !ile 'hich should contain one o! the !ollo'ing possible graph !ile !ormatsJ 1( one line per base and one or more columns o! integer or !loating point &alues per line( The number o! lines should match the number o! bases in the se%uence( "rtemis 'ill plot each data point !or the corresponding base( 8ach column represents a data set !or a line( 8=ample e=tractJ
21+2 22 1D11+G 0 0 1DFG+8 +++ 1D10+G 112N+1 0 0 1GE2+0 N8+2

2( the !irst column corresponds to the base position and is an integer( $ote to distinguish this !ormat !rom the pre&ious !ormat the !irst line o! the !ile must start 'ith a MVM( Line colours can be speci!ied in the header using the Bey'ord colour !ollo'ed by space separated RJGJ9 &alues !or each line( The ne=t ro's0s1 are the data &alues( 8=ample e=tractJ
. A>5< B>?1 B>?2 B>?F B>?2 B>?8 B>?N . colour 8$180$88 288$0$0 0$288$0 0$0$288 100$100$100 80$180$80 1GN 2202+E E2E+2F 0 0 0 8FN+02 2GE E02+DD 0 EFG+2 0 NE1+NF 0 282 0 NDD+DE 0 0 0 281+1E 88F 0 0 0 0 0 82+2 N82 0 0 0 0 FF2+2 0 NEN 0 0 N82+GE 0 0 0 EF1 0 0 0 0 0 NG+DG +++

;( inde=ed tab delimited !ile( -or this tabi= is used 0see the tabi= manual1 to create an inde=( This is especially use!ul !or large data sets as it is memory e!!icient and only reads the data corresponding to the &isible region in "rtemis( The !irst columns contain the se%uence name and base position and this is then !ollo'ed by the &alues to be plotted( -or e=ample M!ile(plotM is a tab delimited !ile 'ith column 1 containing the se%uence name and column 2 the positions/ this is sorted and then inde=ed 'ith tabi=J
,grep -#.# file+plot/ grep -" -#.# file+plot 0 sort -k111 -k212n3 0 bg(ip 4 sorted+plot+g( / tabix -s 1 -b 2 -e 2 sorted+plot+g(

8=ample e=tractJ
foo foo foo foo foo foo +++ 1 2 F 2 8 N 8 1 8 0 8 F0 8 10 1N 2F 22 FN 12D 122 12D 122 121 122 8 12 12 20 2E F2 8 10 18 20 28 F0 2FD 2F2 22D 212 21D 212

3nde=ed user plots can be used 'ith inde=ed -".T" se%uences and inde=ed G-- !iles 0see the section called &e3 ence and Annotation ,ile ,ormats in Chapter 11( The se%uence can then be changed using the drop do'n menu in the 8ntry toolbar and this 'ill change the graph data to the selected se%uence( 4( the ne=t t'o !ormats are types o! 2iggle !ormats( The !irst is &ariable.tep( $ote that "rtemis only supports the colour element in the tracB line(
track t'pe=!iggle_0 color=288120010 "ariable5tep chrom=chr1D span=10 F10 1 F20 12 FF0 1E F20 N F80 8 2F0 F 220 1

Right clicBing on the graph and selecting the MCon!igure(((M option 'ill display the M,lot styleM option !or 'iggle plots( The plots can be displayed as histograms or as a heat map( :( the ne=t !ormat supported by "rtemis is !i=ed.tep and is again a 2iggle !ormat(
track t'pe=!iggle_0 name=#fixed5tep# description=#fixed5tep format# "isibilit'=full auto5cale=off "ie!?imits=0$1000 color=012001100 maxLeight@ixels=100$80$20 graphT'pe=points priorit'=20 fixed5tep chrom=chr1D start=G201 step=F00 span=200 1000 D00 E00 G00 N00 800 200 F00 200 100

( 9last tabular !ormat( The blastall command must be run 'ith the -m U !lag 'hich generates one line o! in!ormation per 4.,( "lternati&ely the 7.,crunch !ile !ormat can be read in as a graph !ile !ormat( "rtemis 'ill prompt the user to determine 'hether it uses the %uery or subHect coordinates to plot the graph( 2hen a !ile is prompted !or there is an option 'hich i! selected 'ill mean the log trans!orm is plotted(

!C Content IKJ
Controls 'hether the GC content plot is &isible( This is a graph o! the a&erage GC content o! a mo&ing 'indo' 0de!ault siIe 120 base1/ across the bases &isible in the o&er&ie' 'indo'( P#e!aultJ o!!Q Pshort nameJ gc_contentQ

!C Content IKJ With 9.: S8 Cutoff

Controls 'hether the cuto!! GC content plot is &isible( This is similar to the GC content graph/ but the

plot is clipped so that the GC content o! each algorithm 'indo' is sho'n only 'hen it is more than 2(: times the standard de&iation o! the GC content in all the 'indo's( P#e!aultJ o!!Q Pshort nameJ sd_gc_contentQ

A! Content IKJ
Controls 'hether the "G content plot is &isible( This is a graph o! the a&erage "G content o! a mo&ing 'indo' 0de!ault siIe 120 base1/ across the bases &isible in the o&er&ie' 'indo'( P#e!aultJ o!!Q Pshort nameJ ag_contentQ

!C .rame /lot
Controls 'hether the GC !rame plot is &isible( This graph is similar to the GC content graph but sho's the GC content o! the !irst/ second and third position independently( -or more in!ormation on the algorithm and on ho' to interpret the result see this 'eb page( .ee 3shiBa'a/ ?( and 4otta/ C( -87. 7icrobiol( Lett( 1<4J2:1-2:; 019991 and GC !rame plot !or more in!ormation on the algorithm( P#e!aultJ o!!Q Pshort nameJ gc_frameQ

Correlation Scores
Controls 'hether the 0!or'ard1 correlation scores plot is &isible( The graph sho's the correlation bet'een the amino acid composition o! the globular proteins in TR879L and the composition o! the base translation in each o! the three reading !rames( The green line represents !or'ard !rame 1/ blue represents !rame 2 and red represents !rame ;( P#e!aultJ o!!Q Pshort nameJ correlation_scoreQ

Re$erse Correlation Scores

This does the same as ACorrelation .coresA/ but does the calculation on the re&erse strand( The green line represents re&erse !rame 1 0the bottom !rame line1/ blue represents !rame 2 and red represents !rame ;( P#e!aultJ o!!Q Pshort nameJ correlation_scoreQ

!C 8e$iation I!0CJ(I!;CJ
Controls 'hether the GC de&iation plot is &isible( This graph sho's the di!!erence bet'een the AGA content o! the !or'ard strand and the re&erse strand( .ee A"symmetric substitution patterns in the t'o #$" strands o! bacteriaA Lobry ?R( - 7ol 9iol 8&ol 199 7ay)1;0:1J 0-:(

P#e!aultJ o!!Q Pshort nameJ gc_de"iationQ

AT 8e$iation IA0TJ(IA;TJ
Controls 'hether the "T de&iation plot is &isible( This graph sho's the di!!erence bet'een the A"A content o! the !or'ard strand and the re&erse strand( P#e!aultJ o!!Q Pshort nameJ at_de"iationQ

6arlin Si"nature 8ifference

This menu item toggles the display o! the graph o! the dinucleotide absolute relati&e abundance di!!erence bet'een the 'hole se%uence and a sliding 'indo'( -or details o! the algorithm see AGlobal dinucleotide signatures and analysis o! genomic heterogeneityA .amuel Carlin - Current 5pinion in 7icrobiology 199U/ 1J:9U- 10( P#e!aultJ o!!Q Pshort nameJ karlin_sigQ

Cumulati$e AT S5e- and Cumulati$e !C S5e"T sBe' is calculated as 0P"Q-PTQ1*0P"QGPTQ1/ 'here P"Q and PTQ are the counts o! these bases in the 'indo'( Grigorie& " 019991 .trand-speci!ic compositional asymmetries in double-stranded #$" &iruses( Eirus Research 0/ 1-19(

/ositional Asymmetry
.hulman 7?/ .teinberg C7/ 2estmoreland $ 019U11 The coding !unction o! nucleotide se%uences can be discerned by statistical analysis( ? Theor 9iol UUJ409-20(

Informational 3ntropy
ConopBa "ndrIeH 019U41 3s the in!ormation content o! #$" e&olutionarily signi!icant> ? Theor 9iol 10<J 9<-<04( 3n!ormational entropy is calculated !rom a table o! o&erlapping #$" triplet !re%uencies/ using e%uation 1 in the abo&e re!erence( The use o! o&erlapping triplets smooths the !rame e!!ect(

Scaled Chi S uare

.hields #C/ .harp ,7 019U<1 .ynonymous codon usage in 9acillus subtilis re!lects both translational selection and mutational biases( $ucleic "cids Res 1:JU02;-40(

Mutational Response Inde)

Gatherer #/ 7c8'an $R 0199<1 .mall regions o! pre!erential codon usage and their e!!ect on o&erall codon bias--the case o! the plp gene( 9iochem 7ol 9iol 3nt 4;J10<-14(

3ffecti$e Codon &umber

2right - 019901 The Me!!ecti&e number o! codonsM used in a gene( Gene U<J2;-9/ and -uglsang " 020041 The Me!!ecti&e number o! codonsM re&isited( 9iochem 9iophys Res Commun( 7ay <);1<0;1J9:<- 4(

Intrinsic Codon 8e$iation Inde)

-reire-,icos 7"/ GonIaleI-.iso 73/ RodrigueI-9elmonte 8/ RodrigueI-Torres "7/ Ramil 8/ Cerdan 78 019941 Codon usage in Cluy&eromyces lactis and in yeast cytochrome c-encoding genes( Gene 1;9J4;-9(

The 8isplay Menu

The buttons in this menu are toggles controlling 'hich parts o! the "rtemis display are &isible( "ll the buttons de!ault to on*acti&e(

Sho- 3ntry 4uttons

This toggle controls 'hether the entry button line is &isible( 0see the section called +he Entry B tton $ine1( P#e!aultJ onQ

Sho- 4ase HieThis toggle controls 'hether the base &ie' is &isible( 0see the section called +he O2er2ie( and DNA 0ie(s1( P#e!aultJ onQ

Sho- .eature List

This toggle controls 'hether the !eature &ie' is &isible( 0see the section called +he ,eat re $ist1( P#e!aultJ onQ

The 3ntry 4utton Line

There is one button on this line !or each currently loaded entry( The buttons indicate 'hich entries are acti&e and allo' the user to toggle each entry bet'een the acti&e and inacti&e states( The de!ault entry can be set by clicBing the right mouse button 0see the section called Notes on !sing +he -o se1 on an entry( .ee also ;/ the section called +he Defa lt Entry in Chapter 1 and the section called +he Acti2e Entries in Chapter 11(

The ,$er$ie- and 8&A Hie-s

The o&er&ie' and #$" &ie' taBe up most o! the main 'indo' 0see the section called A brea)do(n of the main Artemis edit (indo(1( 9oth &ie's act in a &ery similar 'ay/ so they are described in the same section( 3n particular they both sho' the !or'ard and re&erse strands o! the se%uence and a representation o! the three translation !rames in each direction( The !or'ard se%uence is read !rom the 879L entry/ the re&erse se%uence is deri&ed !rom the !or'ard one by complementing it( 3n the o&er&ie' sho's only the stop codons o! each translation !rame/ but in the #$" &ie' the sho's the complete si= !rame translation( The horiIontal scrollbar controls 'hich part o! the se%uence is currently &isible( The scroll bar at the le!t controls the Ioom le&el(

Chan"in" the Selection from a Hie- WindoTo select a !eature Hust clicB on it 'ith the !irst mouse button( This 'ill unselect anything that is currently selected( To add a !eature to the selection rather than replacing the current selection/ hold the shift Bey 'hile clicBing( " single !eature can be remo&ed !rom the selection in the same 'ay/ because shi!t-clicBing acts as a toggle( The situation is made slightly more complicated by the e=istence o! spliced genes( 2hen a !eature segment 0e=on1 is added to the selection the !eature that contains the segment is implicitly added as 'ell( 2hen the last segment o! a !eature is remo&ed !rom the selection/ the !eature is implicitly remo&ed( " single base or amino acid can be selected simply by clicBing on it( " range o! bases can be added by clicBing on the base at one end o! the range then shi!t-clicB on the base at the other end o! the range( "lternati&ely you can drag out a range o! basesJ clicB on a base then hold the mouse button do'n and mo&e to the other end( To select a complete open reading !rame 05R-1/ double clicB the middle mouse button 0see the section called Notes on !sing +he -o se1 any'here inside the 5R- 0see the section called Open Reading ,rame !or another 'ay to select an 5R-1( .ee the section called +he &election in Chapter 1 !or more about the selection(

,ther Mouse Controlled .unctions

#ouble clicBing on a !eature 'ith the !irst mouse button causes both &ie's and the !eature list to centre

themsel&es on that !eature( .imilarly/ double clicBing the !irst mouse button on a base or amino acid 'ill centre both &ie's on that base*amino acid( " double clicB o! the middle mouse button on a !eature 'ill open an edit 'indo' !or that !eature( This is the same as clicBing once and then choosing the 8dit .elected -eatures menu item 0see the section called &elected ,eat res in Editor 1(

The /op0up Menu

The pop-up menu is acti&ated by pressing the third mouse button 0see the section called Notes on !sing +he -o se1 on a !eature &ie'( The menu is split into three sections( The top contains !unctions that 'ill act on the current &ie'( The middle contains shortcuts to some o! the main 'indo' menus( The bottom contains !our toggle buttons 'hich in!luence the appearance o! the &ie'(

/op0up Menu .unctions

$ote that not all o! these !unctions are a&ailable all the time 0the !irst t'o are only sho'n 'hen there are some selected !eatures1( Raise Selected .eatures. Raise the selected !eatures so that they appear in !ront o! all other !eatures( Lo-er Selected .eatures. 7aBe the selected !eatures go behind all the other !eatures( Smallest .eatures In .ront. .ort the &isible !eatures so that the smallest !eatures appear in !ront o! the larger ones( This is only necessary 'hen the user has manually rearranged the !eatures using ARaise .elected -eaturesA or ALo'er .elected -eaturesA( Loom to Selection. .croll and scale the display so that the current selection is centred and !ull 'idth( Select Hisible Ran"e. .elect the currently &isible bases on the !or'ard strand( Select Hisible .eatures. .elect those 0and only those1 !eatures that currently &isible in this &ie'( "ny !eatures that are o!! screen or ha&e been !iltered out 'ith the A.et .core Cuto!!s (((A control( Set Score Cutoffs ... The score cuto!!s panel allo's the user to !ilter the !eatures o! the acti&e entries so that !eatures 'ith lo' or high scores are not sho'n( The AscoreA o! a !eature is the &alue o! the %score %uali!ier and should be a number !rom 0 to 100( The cuto!!s 'indo' has t'o sliders( "ny !eature that has a score less than the &alue o! the top controller or more than the &alue o! the bottom controller 'ill not be sho'n( -eatures 'ith no %score %uali!ier 'ill al'ays be sho'n(

To""le 4uttons
.eature Labels This toggle button controls 'hether the !eature labels are displayed on their o'n line 0'hen the toggle is on1 or on the top o! the !eatures 0'hen the toggle is o!!1( The de!ault setting !or this toggle can be set in the options !ile 0see the section called feature_labels in Chapter 1(

,ne Line /er 3ntry This toggle controls 'hether the entries are sho'n in the conte=t o! the three !rame translation or one entry per line on screen( 3n the !irst case the entries 'ill be o&erlaid/ in second case they 'ill be sho'n in parallel( The de!ault setting !or this toggle can be set in the options !ile 0see the section called one_line_per_entry in Chapter 1(

.or-ard .rame Lines This toggle button controls 'hether or not to sho' the ; !rame translation o! the !or'ard se%uence(

Re$erse .rame Lines This toggle button controls 'hether or not to sho' the ; !rame translation o! the re&erse se%uence(

Start Codons Toggle the display o! start codons in the &ie'( .ee the section called Genetic Code +ables in Chapter 2 to !ind out ho' to change 'hich start codons to use(

Stop Codons Toggle the display o! stop codons in the &ie'(

.eature Arro-s Toggle the display o! directional arro's on each !eature( The de!ault setting !or this toggle can be set in the options !ile 0see the section called draw_feature_arrows in Chapter 1(

.eature 4orders Toggle the display o! blacB borders around each !eature( The de!ault setting !or this toggle can be set in the options !ile 0see the section called draw_feature_borders in Chapter 1(

All .eatures ,n .rame Lines $ormally non-protein !eatures are dra'n on the #$" lines( This toggle allo's the user to !orce all !eatures to be dra'n on the !rame lines/ 'hich can sometimes impro&e readability( The de!ault setting !or this toggle can be set in the options !ile 0see the section called features_on_frame_lines in Chapter 1(

.lip 8isplay 3! selected the se%uence and !eatures 'ill be dra'n on screen as i! they are re&erse complemented 'ith the !irst base to the right o! the screen(

Colourise 4ases This toggle turn base colouring on or o!!( 0$ote that this !eature is completely unless/ it e=ists !or amusement only1(

Scrollin" The Hie7o&ing the horiIontal scrollbar 'ill change the part o! the se%uence that is &isible( The position o! the &ie' can also be changed by using the Goto menu 0see the section called +he Goto -en 1/ by double clicBing the !irst mouse button on a !eature in one o! the se%uence &ie's or in the !eature list or by double clicBing on a base or amino acid(

Chan"in" The Scale

The &ertical scrollbar at the right edge o! the &ie' controls the scale - mo&ing the scrollbar up 'ill Ioom in and mo&ing the scrollbar do'n 'ill Ioom out( 2hen the scrollbar is at the top 0at itMs most AIoomed-inA position1/ the complete si= !rame translation is sho'n( 5ther'ise only the stop codons are sho'n( The main di!!erence bet'een the o&er&ie' and the #$" &ie' is that the #$" &ie' initially sho's the !ull translation/ 'hereas the o&er&ie' sho's only the stop codons( The other di!!erence is that the labels are on in the o&er&ie' by de!ault 0see the section called +he 1op- p -en 1(

28irect 3ditin"2
The direct editing option 0.ee the section called Enable Direct Editing in Chapter 21 enables the user to change the start or end position o! a segment by dragging it around 'ith the mouse( This 'orBs best in the #$" &ie' 'indo'( "s an e=ample/ to mo&e the start position/ clicB the mouse button on the !irst base o! the !eature or e=on/ hold the button do'n/ mo&e the mouse pointer to the desired position/ then release the button(

The .eature List

The !eature list is bit at the bottom o! the main 'indo' o! "rtemis 0see the section called O2er2ie( of the Entry Edit 'indo(1( The !eature list can be toggled on and o!! !rom the display menu 0see the section called &ho( ,eat re $ist1( The same component is used by the t'o items in the &ie' menus that sho' a sub-set o! components 0see the section called CD& Genes And 1rod cts and the section called ,eat re ,ilters1( The list contains in!ormation about each !eature in each acti&e entry 0see the section called +he Acti2e Entries in Chapter 11/ one per line( The lines sho' this in!ormation about the !eatureJ the colour 0see the section called ,eat re Colo rs in Chapter 11/ the Bey/ start base/ end base/ the note !ield 0i! any1 and then the remaining %uali!iers in 879L*G8$9"$C !ormat( 3! the correlation scores option is on then the scores 'ill be sho'n Hust be!ore the note in each C#. line(

Chan"in" the Selection from the .eature List

To select a !eature !rom the list Hust clicB on it 'ith the !irst mouse button( This 'ill unselect anything that is currently selected( To add a !eature to the selection rather than replacing the current selection/ hold the shift Bey 'hile clicBing( " single !eature can be remo&ed !rom the selection in the same 'ay/ because shi!t-clicBing acts as a toggle( .ee the section called +he &election in Chapter 1 !or more about the selection(

,ther Mouse Controlled .unctions

#ouble clicBing on a !eature 'ith the !irst mouse button causes both &ie's and the !eature list to centre themsel&es on that !eature( " double clicB o! the middle mouse button on a !eature 'ill open an edit 'indo' !or that !eature( This is the same as clicBing once and then choosing the 8dit .elected -eatures menu item 0see the section called &elected ,eat res in Editor 1(

The /op0up Menu

The pop-up menu is acti&ated by pressing the third mouse button 0see the section called Notes on !sing

+he -o se1 any'here on the !eature list( The menu contains shortcuts to some o! the main 'indo' menus and three toggle buttonsJ

Sa$e List to .ile

.a&e the list o! !eatures to a !ile(

Sho- Selected 7ualifier

" %uali!ier can be selected to be displayed in the !eature list(

Sho- Correlation Scores

3! this toggle is on the correlation scores !or each !eature 'ill be sho' bet'een the end base and the note(

Sho- !ene &ames

This button controls 'hether the Bey or gene name is sho'n !or each !eature( The Agene nameA is actually the %label %uali!ier o! the !eature( 3! there is no %label then the %gene %uali!ier is used( 3! neither o! the %uali!iers e=ists then the Bey is used(

Sho- 7ualifiers
3! this option is on the !eature %uali!iers 'ill be displayed a!ter the note(

Sho- /roduct
This button controls 'hether the %note or %product is sho'n !or each !eature( Pde!aultJ %note Q

Scrollin" The List

The scrollbar on the right o! the list controls 'hich part o! the list o! acti&e !eatures is &isible( The list 'ill also mo&e i! the user double clicBs on a !eature in o&er&ie' or #$" &ie' areas/ in 'hich case the list 'ill scroll to that !eature(

!raphs and /lots

The #$" plots are accessed !rom the Graph menu 0see the section called +he Graph -en 1( 2hen a graph is turned on it is locBed to the o&er&ie' 'indo'/ so it 'ill !ollo' the o&er&ie' 'indo' 'hen the o&er&ie' is scrolled( 3t 'ill also automatically change the &ie'ing scale to match the scale o! the o&er&ie' 'indo'( The &ertical scrollbar to the right o! the graph controls the 'indo' siIe o! algorithm( The !eature plots 'indo' 0see the section called ,eat re 1lots1 has a horiIontal scroll bar that sets the position o! the plot in the !eature( "s 'ith the #$" plots/ the &ertical scrollbar to the right o! the graph controls the 'indo' siIe o! algorithm( $ote that clicBing the le!t mouse button on the plot 'ill sho' the base or residue at that position( ClicBing the right mouse button 'ill pop-up a menu( The menu contains a toggle 'hich controls 'hether the graph is scaled and some menu items 'hich allo' the ma=imum 'indo' siIe to be set(

Annotation Halidation
Go- to Run Halidation Chec5s
"rtemis can carry out &alidations checBs to try and minimise annotation errors( These checBs can be carried out in the !ollo'ing 'aysJ 1( ClicB on the ticB button !ound in the top right hand side o! "rtemis to &alidate all !eatures( 2hen complete it 'ill open a report 'indo' highlighting any !eatures 'hich ha&e !ailed the checBs( 2( .elect the !eatures to be checBed in "rtemis and open the popup menu by right clicBing on the !eature display and selecting the MEalidation report (((M option( ;( -rom the Eie' menu/ select the M-eature -iltersM menu item and the MEalidation checBs(((M option( This opens a !eature list 'indo' !or each o! the type o! checB it carries out and these contain the !eatures that ha&e !ailed the checB( 4( -or organisms in a chado database the &aidator can be run !rom the M#atabase and -ile 7anagerM 'indo' !rom the M-ileM menu by selecting the MEalidate .elected .e%uence * 5rganismM option(

Halidation Chec5s .or All .ile Types

The !ollo'ing checBs are made on all !ile types 0e(g( 879L/ G--;1J C#. ha&e no internal stop codon C#. ha&e a &alid stop codon "dditionally "rtemis checBs G5 annotation !orJ

 une=pected 'hite space in 'ith*!rom and db=re! columns the 23T4*-R57 !ield must be empty 'hen using 3#"/ $"./ $#/ T". or 8@, e&idence code G5J000::1: can only ha&e 3,3 e&idence code 38, is not allo'ed !or molecularK!unction and cellularKcomponent terms the 23T4*-R57 !ield must be !illed 'hen using 3../ 3."/ 3.5 and 3.7 codes

Halidation Chec5s .or !..@

The !ollo'ing are checBs !or G--; and Chado entries onlyJ checB that the gene model comprises o! at least a gene and a transcript !eature checB that the boundaries o! the !eatures maBing up a gene model are consistent checB that all the !eatures in a gene model are on the same strand checB that C#. !eatures ha&e a phase checB the attribute column to ensure that %uali!iers ha&e a &alue 0not empty1 and that only reser&ed tags start 'ith an uppercase character checB that partial %uali!iers are consistent 'ithin a gene model checB that the gene name pre!i= is consistent 'ithin a gene model

Halidation Report
The &alidation report 'indo' displays a summary !or the !eatures that ha&e !ailed one or more o! the annotation checBs abo&e( The title bar o! the 'indo' displays the number o! !eatures that ha&e passed and the number that ha&e !ailed the &alidation checBs( The problems identi!ied are highlighted in red(

.ome o! the errors can be !i=ed automatically( The M"uto--i=M button opens a 'indo' 'ith the !i=es enabled that are a&ailable !or the entry type that is loaded in "rtemis( -or e=ample/ it 'ill attempt to !i= C#. !eatures that ha&e been !ound not to end in stop codons( 3! the last codon is not a stop codon/ but the &ery ne=t codon is a stop codon/ then the end o! the !eature is e=tended by three bases( -or G--; and chado entries "rtemis 'ill also attempt to !i= problems it !inds 'ith gene boundaries and i! a phase is absent then a de!ault phase o! 0 is gi&en( 5nce these are !i=ed the results 'indo' 'ill automatically update and remo&e the problems it has managed to resol&ed(

&otes on %sin" The Mouse

"rtemis maBes use o! all three buttons o! the mouse under @/ but other 'indo'ing systems o!ten ha&e less than three buttons( To maBe li!e easier 'hen running "rtemis on those systems/ there are some alternati&e Bey bindings( 5n 2indo's pressing the alt or meta Bey and the !irst mouse button 'ill gi&e the same e!!ect as pressing mouse button three 0usually a pop-up menu1( ,ressing the control Bey and the !irst mouse button 'ill do the same thing as mouse button t'o( 5n 7acintosh systems pressing the control Bey and the mouse button 'ill gi&e the same e!!ect as pressing mouse button three 0usually a pop-up menu1( ,ressing the alt Bey and the mouse button 'ill do the same thing as mouse button t'o(

Chapter A. /ro=ect .ile Mana"er ,$er$ieThe ,roHect -ile 7anager can be used to !acilitate the launching o! groups o! !iles together( The proHect details are stored bet'een sessions o! "rtemis/ so that it is straight!or'ard to return to a proHect and open up all the rele&ant !iles(

%sin" the /ro=ect .ile Mana"er

The ,roHect -ile 7anager can be opened !rom the ,ile menu in the "rtemis launch 'indo' 0see the section called +he Artemis $a nch 'indo( in Chapter 21( 3t opens 'ith some e=ample proHects in the list on the le!t hand side o! the panel( .electing a proHect in the list sho's the associated !iles in the right hand side o! the 'indo'( To add a ne' proHect clicB on the green MGM button at the top o! the ,roHect -ile 7anager 'indo' and enter a name !or the proHect( The ne' proHect opens 'ith a blanB !orm 'ith a Mse%uenceM !ield( Note that each pro7ect has to ha2e an associated se3 ence file 4e.g. ,A&+A8 E-B$8 GenBan) or G,,6 that contains the n cleotide se3 ence for Artemis to open p. $e' !iles can be added to the proHect by selecting the type o! !ile !rom the drop do'n list at the bottom and clicBing the M$82 ,R5,8RT6M button( The proHect list and details are sa&ed bet'een sessions 'hen "rtemis is closed do'n( This in!ormation is stored in the home directory in a !ile called M(artemis(proHect(propertiesM( 2hen "rtemis is run it looBs !or a MproHect(propertiesM !ile in the local directory as 'ell as !or the M(artemis(proHect(propertiesM !ile in the home directory( 9e!ore opening a proHect the !iles can be toggled on and o!! in the ,roHect -ile 7anager so that each can optionally be deselected and not opened( 5nce a proHect has been set up it can be selected !rom the list and clicBing M5,8$M 'ill open the main "rtemis 'indo'(

To remo&e a proHect !rom the list/ select the proHect name and clicB the red M-M button at the top o! the 'indo'(

Chapter :. Secure Shell ISSGJ /lu"in To Artemis ,$er$ie- of the SSG /lu"in
This is a plug-in to "rtemis that enables you to &ie' and trans!er !iles !rom a local machine 0e(g( ,C*7ac5.@*+$3@1 to another remote !ile system 0i(e( any other !ile system that you ha&e ssh access to1( The main areas 'here this is use!ul areJ !ile management !or both local and remote !iles( -iles can be trans!erred by dragging and droping bet'een !ile systems( 7ultiple !iles can be selected and trans!erred in this 'ay( launching "rtemis and "CT 'ith se%uences and tab !iles !rom !iles on the remote machines( running 9L".T and -asta searches can be sent !rom the local machine that is running "rtemis and run on the remote machine( To do this the so!t'are 09L".T and -asta1 need to be set up on the remote side 0see the section called Config ring &earches to be r n 2ia &&91(

Lo"in In
-rom the "rtemis launch 'indo' go to the M-ileM menu and select M5pen ..4 -ile 7anagerM( " !ile manager 'indo' 'ill then open 'ith a local !ile manager at the top( +nderneath this is a remote !ile manager 'ith a section to enter login details(

3! you can connect directly to the remote machine gi&e the hostname/ username and pass'ord( "lternati&ely i! you are using a ..4 tunnel 0see the section called &etting p a &&9 t nnel1 then use localhost and the appropriate port number(

Settin" up a SSG tunnel

The tunneling capability o! ..4 .ecure .hell allo's people to access their email/ intra'eb pages and !iles securely e&en 'hen 'orBing a'ay !rom the o!!ice( This can be used 'ith "rtemis and this section pro&ides some e=amples o! setting up tunnelling( 3t may be necessary to consult your !riendly system administrator about the details on ho' best to do this( 5n !NI" the ssh con!iguration can be set in the !ile *%+ssh%config( This contains the in!ormation to set up a tunnel that looBs liBe thisJ
Lost U+sanger+ac+uk

?ocalFor!ard 2222 machine+sanger+ac+uk$22 ;ser tMc

5nce this con!iguration !ile is in place you can login !rom a +$3@ 'indo' to set up a tunnel( 5n 'indo(s you can use ,utty/ see the section called !sing 1 tty to &et !p A + nnel( 2hen the tunnel has been established you can start artemis and enter MlocalhostM into the 4ostname !ield in the login 'indo' and the port number 0e(g( 2222 in the abo&e e=ample1(

The !ile manager can be used to drag and drop !iles bet'een each !ile system( 3! you right clicB on a selected !ile this 'ill pro&ide you 'ith a pop-up menu 0see belo'1 enabling you to delete/ rename and open !iles(

-iles on the remote !ile system can be double clicBed on and opened in "rtemis 0in the same 'ay they can be opened !rom the local !ile manager1( Tab !iles can be read in by dragging them !rom the remote !ile manager and dropping them into the "rtemis 'indo'( $ote !or "CT the se%uence !ilename can be dragged !rom the !ile manager into the !ile selection bo= 0i! the !iles are not !ound locally the are then located on the ser&er1( The tab !iles in "CT can be dragged !rom the !ile manager and dropped on the rele&ant se%uence display( 2hen !iles are sa&ed/ i! the entry orginated !rom the remote !ile system then this is sa&ed locally in the current 'orBing directory and to the remote !ile as 'ell(

%sin" /utty to Set %p A Tunnel

5n 'indo(s you can use ,utty to set up a ssh tunnel( 9elo' are settings that can be used in ,utty to set up a ..4 tunnel(

..4 2 only is probably recommended here(

@11 !or'arding is not necessary(

.et the source port to 2222 and set the destination to hostnameJport 0e(g( pcs2(internal(sanger(ac(uBJ221(

ClicB M"ddM to add this to the list o! !or'arded ports(

Run "rtemis and select the M..4 -ile 7anagerM !rom the M-ileM menu( "t the bottom !ill in login details and clicB on the MConnectM button( Loging in may taBe a minute 0depending on the connection1(

%sin" the SSG connection to run .asta and 4LAST

+sing the ..4 connection you can send -asta and 9L".T searches to be run on the remote machine( 3! you ha&e not already be prompted to login 0i(e( 'hen opening up the ..4 !ile manager1/ you 'ill then be asBed !or your login details( The se%uence !iles that are to be searched against the database are then sent to the remote machine( 5nce the search has !inished the results are trans!erred bacB a!ter'ards( 3! "rtemis detects that you ha&e opened up an entry !rom the remote !ile system the analysis 'ill be run in the directory you open the entry !rom( The results in this case are stored on both the local and remote machines( To Beep -asta and 9L".T searches on your local machine and the remote !ile system in-syncJ copy any pre&iously run !asta and blast directories !rom the remote machine to your local !ile system( This can be done by maBing a tar ball o! the directoryJ e(g( creating a tar !ile o! a M!astaM directory

tar c"f tar_ball_name+tar fasta

Then trans!er this !ile to the local proHect directory and e=tract 'ithJ
tar x"f tar_ball_name+tar

'hen launching "rtemis/ maBe sure you !irst change directory to the directory abo&e the M!astaM directory that has been unpacBed( open the !iles !rom the remote !ile system in the !ile manager( 3t then Bno's 'here to sa&e it bacB to(

Confi"urin" Searches to be run $ia SSG

This 'ould most liBely be done by a systems administrator( The databases and !asta and 9L".T so!t'are need to be set up on the remote machine( 5nce this is done the commands that are sent !rom the "rtemis*"CT client to the remote machine are controlled by a MH2ssh(propertiesM !ile/ see belo' !or e=ample o! this !ile( This needs to be put in the CL"..,"T4 !or "rtemis*"CT or the one in the distribution 0lib*H2ssh*H2ssh(properties1 modi!ied( The H2ssh(properties !ile also hold de!ault in!ormation( -or e=ample de!ault parameters can be set !or the login prompt/ the 'orBing directory 0!or searches 'hen se%uences are opened on the local side1 and any e=tra directories 0other than the users home directory1 to display in the !ile manager(
. . . onfiguration file for using 55L file management and . database searches+ . . . default login options port=2222 host=localhost . . . 9eneric default options . blastp=blastall -p blastp blastx=blastall -p blastx tblastx=blastall -p tblastx blastn=blastall -p blastn fasta=fastaFF_t -A -5 -) -b 100 -L -l %data%fasta%pubse)gbs fastx=fastxFF_t -A -5 -) -b 20 -L -l %data%fasta%pubse)gbs . . . default !orking director' !dir=%scratch . . . aliases used for fasta Vuniprot=V; Vuniprot_archaea=V> Vuniprot_bacteria=VA Vuniprot_eukar'ota=V< Vuniprot_"iruses=VB Vuniprot_rest=V= Vmalaria=V6 Vkineto_aa=VO default_db=Vuniprot_bacteria

. . . remote directories to use as roots in the file manager remotedir+@D=%nfs%pathdata remotedir+I@=%nfs%disk222%'eastpub . local directories to use as roots in the file manager localdir+@D=%nfs%pathdata localdir+I@=%nfs%disk222%'eastpub

Chapter C. Artemis Confi"uration ,ptions The ,ptions .ile

2hen started on "rtemis 'ill potentially looB in : di!!erent places !or !iles to e=amine !or con!iguration in!ormation( "rtemis reads !rom the locations in order/ so the user can o&erride the de!ault options( $ote that on 7acintosh and 2indo's systems the Acurrent directoryA mentioned belo' is the directory 'here the "rtemis application has been installed( This is the search orderJ The standard "rtemis options are read !irst( 5n +$3@ this !ile is in the !ile etc%options in the "rtemis distribution directory( Changing that !ile 'ill change the options settings !or all users( 5n 7acintosh and 2indo's system the standard options are stored in the "rtemis application itsel! and canMt be changed 0easily1( 3! the user has speci!ied an options !ile on the command line 'ith the -options argument/ it 'ill be read ne=t( 0+$3@ only - see the section called !NI" Command $ine Arg ments for Artemis in Chapter 2 !or more1( 3! there is a !ile called diani+ini in the current directory it 'ill be read( This is !or bacB'ards compatibility( 3! there is a !ile called options/ options+txt or options+text in the current directory it 'ill be read( 3! there is a !ile in the userMs home directory called +artemis_options it 'ill be read(

Artemis ,ption 8escriptions

This section describes the possible options !or "rtemis(

font_si(e
This option 'ill set the !ont siIe !or all the "rtemis 'indo's( Pde!aultJ 14Q

font_name
This option is used to choose the !ont !or all the "rtemis 'indo's( The !ont must be !i=ed-'idth( Pde!aultJ A7onospacedAQ

base_plot_height
The height 0in pi=els1 o! each o! the base plots( Pde!aultJ 1:0Q

feature_plot_height
The height 0in pi=els1 o! each o! the !eature plots( Pde!aultJ 1 0Q

dra!_feature_borders
3! set to yes/ borders 'ill be dra'n around each !eature and each e=on( i! set to no/ borders 'ill only be dra'n around the selected !eatures( This can also be set in the &ie's popup menu 0see the section called ,eat re Borders in Chapter ;1( Pde!aultJ AyesAQ

sho!_for!ard_lines
3! set to yes/ the !or'ard !rame lines are sho'n by de!ault( This can also be set in the &ie's popup menu( Pde!aultJ AyesAQ

sho!_re"erse_lines
3! set to yes/ the re&erse !rame lines are sho'n by de!ault( This can also be set in the &ie's popup menu( Pde!aultJ AyesAQ

dra!_feature_arro!s
3! set to yes/ a direction arro' 'ill be dra'n around at the end o! each !eature( i! set to no/ no arro's 'ill be dra'n( This can also be set in the &ie's popup menu 0see the section called ,eat re Arro(s in Chapter ;1( Pde!aultJ AyesAQ

o"er"ie!_feature_labels
3! this option is no then the !eature labels in the o&er&ie' 0see the section called O2er2ie( of the Entry Edit 'indo( in Chapter ;1 'ill be o!! at startup( Pde!aultJ AyesAQ

o"er"ie!_one_line_per_entr'
3! this option is set yes then the o&er&ie' 0see the section called O2er2ie( of the Entry Edit 'indo( in Chapter ;1 'ill start in one line per entry mode( Pde!aultJ AnoAQ

sho!_list
3! set to yes then the !eature list 0see the section called +he ,eat re $ist in Chapter ;1 'ill be sho'n on startup( Pde!aultJ AyesAQ

sho!_base_"ie!
3! set to yes then the #$" base &ie' 0see the section called +he O2er2ie( and DNA 0ie(s in Chapter ;1 'ill be sho'n on startup( Pde!aultJ AyesAQ

features_on_frame_lines
3! set to yes then the A"ll -eatures 5n -rame LinesA option 'ill be set to yes on startup( 0.ee the section called All ,eat res On ,rame $ines in Chapter ;1 Pde!aultJ AnoAQ

frame_line_features
This is a list o! the !eature Beys that should be sho'n by de!ault on the !rame lines( e(g(
frame_line_features = D5 W pol'peptide W

feature_labels
3! set to yes then the !eature labels 'ill be sho'n on startup( 0.ee the section called All ,eat res On ,rame $ines in Chapter ;1 Pde!aultJ AyesAQ

one_line_per_entr'
3! set to yes then the A5ne Line ,er 8ntryA option 'ill be set to yes on startup( 0.ee the section called All ,eat res On ,rame $ines in Chapter ;1 Pde!aultJ AnoAQ

genetic_codes
This option gi&es the list o! names o! the a&ailable genetic code tables( -or each name in the list there is a translationKtableK$+798R entry 0see belo'1 'here $+798R is its location in the geneticKcodes list( .imilarly the start codons are de!ined as startKcodonsK$+798R !or each code(

translation_table_1
The translationKtable option is used to looBup codon translations( The table must ha&e e=actly 4 entries/ and there is one entry !or each codon( The entries should appear in this orderJ
TTT TT T T T +++ TT> TT9 +++

This is the de!ault setting !or this option is the .tandard CodeJ
translation_table_1 = W f f l l W s s s s W ' ' U U W c c U ! W W l l l l W p p p p W h h ) ) W r r r r W W i i i m W t t t t W n n k k W s s r r W W " " " " W a a a a W d d e e W g g g g

The other translation table entries are de!ined by gi&ing the di!!erences to the .tandard Code( These are gi&en as the bases that maBe up the codon immediately !ollo'ed by the translation 0e(g( atam/ so that MataM codes !or MmM1(

extra_ke's
This contains a list o! Beys 0separated by spaces1 that are allo'ed in addition to those speci!ied by 879L( The o!!icial 879L Beys are listed in the feature_ke's !ile in the "rtemis code directory(

extra_)ualifiers
This contains a list o! %uali!iers 0and their associated type1 that are allo'ed in addition to those speci!ied by 879L( The o!!icial 879L %uali!iers and %uali!ier types are listed and described in the )ualifier_t'pes !ile in the "rtemis code directory(

common_ke's
This is a list o! the Beys that should be sho'n by de!ault in the !eature edit 'indo'( 0see the section called &elected ,eat res in Editor in Chapter ;1( The de!ault setting !or this option isJ
common_ke's = W allele attenuator D5 conflict exon intron ?T= misc_feature misc_=:> m=:> W mutation pol'>_signal pol'>_site promoter protein_bind =A5 repeat_region W repeat_unit r=:> sc=:> sn=:> source stem_loop 5T5 T>T>_signal terminator W t=:> unsure "ariation -10_signal -F8_signal D5_motif gene W A?>5T:_L7T D5_A<FK=< D5_>FT<= A?>5T D5

h'perlinks
This is a list o! databases and their +RLMs !or "rtemis to pro&ide hyperlinBs in the -eature 8ditor 0see the section called &elected ,eat res in Editor in Chapter ;1(

undo_le"els
The number o! le&els o! undo to sa&e or 0 to disable undo( 7ore undo le&els 'ill re%uire more memory( Pde!aultJ 20Q

minimum_orf_si(e
This option is used to set the minimum siIe 0in amino acid residues1 o! a AlargeA open reading !rame/ 'hich controls 'hich 5R-. are marBed by the A7arB 5pen Reading -ramesA menu item 0see the section called -ar) Open Reading ,rames ... in Chapter ;1(

direct_edit
.et the de!ault &alue !or the direct edit option( " &alue o! AyesA 'ill turn direct edit on by de!ault( .ee the section called Enable Direct Editing in Chapter 2

feature_dna_programs
This is a list o! the possible e=ternal programs that can be run on the bases o! a !eature( 8ach pair in the list is a program name and a de!ault database to use !or that program( -or each program name there must be a corresponding shell script called ArunKsomethingA( eg( runKblastn( .ee the section called Config ring the R n -en in Chapter ; !or more in!ormation(

feature_protein_programs
This is a list o! the possible e=ternal programs that can be run on the translation o! a !eature( 8ach pair in the list is a program name and a de!ault database to use !or that program( -or each program name there must be a corresponding shell script called ArunKsomethingA( eg( runKblastp !or blastp or runK!asta !or !asta( .ee the section called Config ring the R n -en in Chapter ; !or more in!ormation(

ncbi_dna_search
This lists the $C93 'eb-9L".T applications that the bases o! a selected !eature can be sent to( .ee the section called +he R n -en in Chapter ;(

ncbi_protein_search
This lists the $C93 'eb-9L".T applications that the translation o! a selected !eature can be sent to( .ee the section called +he R n -en in Chapter ;(

Settin" Colours
The !eature colours 0see the section called ,eat re Colo rs in Chapter 11 used by "rtemis can be changed using the options !ile( 9y de!ault there are 1U possible colours 0numbered 0 to 1<1/ but any number can be used( The option names !or the colours are colour_0/ colour_1/ etc( The &alue o! each o! these %uali!iers should be the three numbers separated by spaces( The numbers correspond to red/ green and blue respecti&ely and each number is an intensity !rom 0 to 2::( "s an e=ample/ to change colour 2 to 'hite put this line in the options !ileJ

colour_2 = 288 288 288

4ere is a list o! the de!ault colour numbersJ

0 1 2 F 2 8 N G E D 10 11 12 1F 12 18 1N 1G !hite dark gre' red green blue c'an magenta 'ello! pale green light sk' blue orange bro!n pale pink light gre' black mid red$ light red pink ,=9A ,=9A ,=9A ,=9A ,=9A ,=9A ,=9A ,=9A ,=9A ,=9A ,=9A ,=9A ,=9A ,=9A ,=9A ,=9A ,=9A ,=9A "alues$ "alues$ "alues$ "alues$ "alues$ "alues$ "alues$ "alues$ "alues$ "alues$ "alues$ "alues$ "alues$ "alues$ "alues$ "alues$ "alues$ "alues$ 288 100 288 0 0 0 288 288 182 1F8 288 200 288 1G0 0 288 288 288 288 100 0 288 0 288 0 288 281 20N 1N8 180 200 1G0 0 NF 12G 1D1 2883 1003 03 03 2883 2883 2883 03 1823 2803 03 1003 2003 1G03 03 NF3 12G3 1D13

,ptions .or /lots and !raphs

8ach graph type has three option settings associated 'ith itJ the de!ault minimum 'indo' siIe/ de!ault ma=imum 'indo' siIe and the de!ault 'indo' siIe( The option names ha&e the !ollo'ing !ormJ Sshort_nameT_default_min_!indo!/ Sshort_nameT_default_max_!indo! and Sshort_nameT_default_!indo! 0respecti&ely1( Sshort_nameT should be replaced 'ith the short name o! the graph( 0The a&ailable short names are documented in the section called +he Graph -en in Chapter ; and the section called ,eat re 1lots in Chapter ;1( "s an e=ample the short name o! the GC content graph is gcKcontent so to set the initial minimum 'indo' siIe to 100/ the ma=imum to 1000 and the initial 'indo' siIe to 1:0 use these settingJ
gc_content_default_min_!indo! = 100 gc_content_default_max_!indo! = 1000 gc_content_default_!indo!_si(e = 180

.ee also the section called Graphs and 1lots in Chapter ;(

,ptions .or A Chado 8atabase

chado_exon_model
This is the !eature Bey used 'hen chado e=ons are Hoined and displayed in "rtemis( -or e=ampleJ
chado_exon_model= D5

Pde!aultJ Ae=on-modelAQ

chado_transcript
This is the !eature Bey used 'hen chado transcripts are created in a gene model( Pde!aultJ AmR$"AQ

chado_ser"ers
This can be used to pro&ide a list o! a&ailable databases( -or e=ampleJ
chado_ser"ers = W test localhost$82F2%test&user:ame W genedb_ro db+genedb+org$82F2%snapshot&genedb_ro

,ptions .ile .ormat

The option !iles it should contain settings that looB liBe thisJ
option_name = option_"alue

3! the &alue o! an options is too long to !it on one line it can be split o&er se&eral lines by ending each line 'ith a bacBslash liBe thisJ
option_name = option_"alue another_option_"alue W a_third_option_"alue a_forth_option_"alue

An 3)ample ,ptions .ile

4ere is an e=ample options !ileJ
. this line is a comment font_si(e = 12 minimum_orf_si(e = 100 common_ke's = W allele attenuator D5 conflict exon intron ?T= misc_feature misc_=:> m=:> W mutation pol'>_signal pol'>_site promoter protein_bind =A5 repeat_region W repeat_unit r=:> sc=:> sn=:> source stem_loop 5T5 T>T>_signal terminator W t=:> unsure "ariation -10_signal -F8_signal D5_motif gene