S Y B Sc Bioinformatics Principles of Sequence Analysis MCQ Test -1 Date: 6/8/12 Total Marks: 30

1. Which of the following is applicable to D ! se"#ence$ a% &earching restriction en'()e recognition sites b% &earching for acti*e sites of en'()e c% &t#+( of post translational )o+ifications +% &earching h(+rophobic regions 2. ,rotein se"#ence anal(sis in*ol*es a% &earching conser*e+ sites b% &earching signal clea*age sites c% -(+rophobic region pre+iction +% !ll of the abo*e 3. The relationship.s% between se"#ences in sets of )ore than two se"#ences can be st#+ie+ b( a% Dot )atri/ b% D(na)ic progra))ing c% M#ltiple se"#ence align)ent +% 01!&T 2. What is first step of ph(logenetic anal(sis$ a% Do)ain i+entification b% ,attern searching c% M#ltiple se"#ence align)ent +% &)ith water)an algorith) 3. What is one t(pe of ho)olog($ a% !nalog( b% ,aralog( c% 4enolog( +% one o#t of the) 6. &e"#ences are sai+ to be orthologo#s if a% The( ha*e co))on ancestor b% The( e)erge+ b( gene +#plication c% The( #n+ergo con*ergent e*ol#tion +% The( #n+ergo gene transfer 5. 6ene +#plication can gi*e rise a% !nalogo#s se"#ences b% ,aralogo#s se"#ences c% 4enologo#s se"#ences +% 7rthologo#s se"#ences

8. &i)ilar acti*e site between two proteins s#btilisin an+ chi)otr(psin is an e/a)ple of a% 8o))on ancestr( b% 8on*ergent e*ol#tion c% Trans+#ction +% 6ene +#plication 9. -ori'ontal gene transfer an+ trans+#ction e*ents are associate+ with a% 7rtholog( b% !nalog( c% ,aralog( +% one of abo*e 10.Which +atabase is a 6ene +atabase with all annotation$ a% 80: 6ene b% 80: 6en0ank c% ;ni,rot +% 80: 6eno)e ,ro<ect 11.Which of the following +atabase is +eri*e+ fro) )= ! infor)ation$ a% +b>&T b% ,D0 c% 7M:M +% -T6& 12.What is the +ifference between =ef&e" an+ 6en0ank$ a% =ef&e" incl#+es p#blicl( a*ailable D ! se"#ences s#b)itte+ fro) in+i*i+#al laboratories an+ se"#encing pro<ects b% 6en0ank pro*i+es nonre+#n+ant c#rate+ +ata c% 6en0ank se"#ences are +eri*e+ fro) =ef&e" +% =ef&e" se"#ences are +eri*e+ fro) 6en0ank an+ pro*i+e nonre+#n+ant c#rate+ +ata 13.Which )etho+ is 7T a pairwise align)ent )etho+$ a% Wor+ / k?t#ple base+ )etho+ of ho)olog( searching b% D(na)ic progra))ing c% Dot )atri/ +% one of abo*e 12.Which of the following )etho+ pro*i+es eas( to interpret graphical o#tp#t for se"#ence align)ent$ a% D(na)ic progra))ing b% Dot )atri/ c% 8l#stalW +% ,attern searching 13.&li+ing win+ow )etho+ is associate+ with a% 8l#stalW b% Dot )atri/ c% D(na)ic progra))ing +% 01!&T

16.@or +ot )atri/A what wo#l+ (o# select to co)pare highl( si)ilar large D ! se"#ences$ a% Win+ow si'e: 10 an+ c#toff: 8 b% Win+ow si'e: 10 an+ c#toff: 6 c% Win+ow si'e: 3 an+ c#toff: 3 +% Win+ow si'e: 3 an+ c#toff: 0 15.Dot )atri/ is )ainl( #se+ for a% :+entif( si)ilarit( between two se"#ences b% ,re+ict secon+ar( str#ct#re of = ! c% !nal('e se"#ence repeats in e#kar(otes +% !ll of abo*e 18. Which )etho+ can g#arantee opti)al align)ent$ a% Dot )atri/ b% D(na)ic progra))ing c% 01!&T +% 8l#stalW 19. :nsertions an+ +eletions in se"#ence can be score+ b( a% ,!M 20 b% ,!M 230 c% 017&;M 62 +% one of abo*e 20.Which scoring )atri/ sho#l+ be chosen to align two highl( +i*ergent se"#ences$ a% ,!M 20 b% ,!M 230 c% 017&;M 62 +% 017&;M 80 21.,!M series of )atrices are b#ilt on a% >*ol#tionar( )o+el b% ,rotein conser*ation c% 8on*ergent e*ol#tionar( st#+ies +% 6ene transfer )echanis) 22.Which is )ost )#table a)ino aci+ accor+ing to ,!M )atri/$ a% 6l#ta)ine b% 8(stein c% &erine +% Tr(ptophan 23.Which is least )#table a)ino aci+ accor+ing to ,!M )atri/$ a% !spargine b% 6l#ta)ine c% 1e#cine +% -isti+ine

22.The ,!M230 )atri/ is +efine+ as ha*ing an e*ol#tionar( +i*ergence in which what percentage of a)ino aci+s between two ho)ologo#s se"#ences ha*e change+ o*er ti)e$ a% 1B b% 20B c% 80B +% 230B 23.-ow +oes the 017&;M )atri/ +iffer )ost notabl( fro) ,!M )atri/$ a% :t is +eri*e+ fro) large n#)ber of protein fa)ilies b% :t is base+ on global )#ltiple align)ent fro) closel( relate+ proteins c% :t is base+ on local )#ltiple align)ent fro) closel( relate+ proteins +% :t co)bines local an+ global align)ent infor)ation 26.Which scoring )atri/ is #se+ as a +efa#lt scoring sche)e in 01!&T$ a% 017&;M 80 b% ,!M 230 c% ,!M 1 +% 017&;M 62 25.,ro*i+e+ 6ap opening penalt( .6%A 6ap e/tension penalt( .1% an+ n#)bers of gap .n%A Total gap score is gi*en b( a% 6ap score C 6 D 1n b% 6ap score C 6n D 1 c% 6ap score C 61 D n +% 6ap score C 6 D 1 D n 28.Two protein se"#ences that share 30B i+entit( are 30B ho)ologo#s a% Tr#e b% @alse 29.=easonabl(A (o# ha*e short +o#ble stran+e+ D ! se"#ence. -ow )an( proteins can it potentiall( enco+e$ a% 1 b% 2 c% 3 +% 6 30.&elect the tr#e arrange)ent in case of +(na)ic progra))ing a% :nitiali'ationA trace backA )atri/ filling b% Trace backA )atri/ fillingA initiali'ation c% Matri/ fillingA initiali'ationA trace back +% one of abo*e