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M.Prasad Naidu
MSc Medical Biochemistry,
There are unique requirements for implementing algorithms for sequence

The first criterion is SENSITIVITY, which refers to the ability to find as many
correct hits as possible.

The second criterion is SELECTIVITY, also called SPECIFICITY, which refers

to the aility to e!clude incorrect hits.
These incorrect hits are unrelated sequences mistakenly identified in database
searching and are considered false positives.

The third criterion is SPEED, which is the time it ta"es to #et results from
data base searches.
Depending on the size of the database, speed sometimes can be a primary
n increase in sensitivity is associated with decrease in selectivity.
n improvement in speed often comes at the cost of lowered sensitivity and
!n database searching, as well as in many other areas in bioinformatics, are two
fundamental types of algorithms.

"ne is the exhaustive type, which uses a rigorous algorithm to find the best or
e#act solution for a particular problem by e#amining all mathematical
Dynamic programming is an example of the e#haustive method and is
computationally very intensive.

nother is the heuristic type, which is a computational strategy to find an

empirical or near optimal solution by using rules of thumb.
The shortcut strategy followed by this type is not guaranteed to find
the best or most accurate solution.
!t is often used because of the need for obtaining results within a realistic time
frame without significantly sacrificing the accuracy of the computational output.
$earching a large database using the dynamic programming methods, such as the
$mith%&aterman algorithm, although accurate and reliable, is too slow and
impractical when computational resources are limited.
'g( querying a database of )**,*** sequences using a query sequence of +**
residues takes ,%) hours to complete with a regular computer system at the time.
Thus, speed of searching became an important issue. To speed up the comparison,
heuristic methods have to be used.
The heuristic algorithms perform faster searches because they e#amine only a
fraction of the possible alignments e#amined in regular dynamic programming.
-oth -.$T and /$T use a heuristic word method for fast pairwise sequence
!t works by finding short stretches of identical or nearly identical letters in two
sequences. These short strings of characters are called words.
The basic assumption is that two related sequences must have at least one word in
"nce regions of high sequence similarity are found, ad0acent high1scoring regions
be 0oined into a full alignment.
The -.$T program was developed by $tephen ltschul of 23-! in +44*.
-.$T uses heuristics to align a query sequence with all sequences in a
The ob0ective is to find high1scoring ungapped segments among related
-.$T performs sequence alignment through the following steps.
The first step is to create a list of words from the query sequence. 'ach
word is typically three residues for protein sequences and eleven residues for
D2 sequences.
The list includes every possible word e#tracted from the query sequence. This
step is also called seeing.
The secon step is to search a sequence database for the occurrence of
these words. This step is to identify database sequences containing the
matching words.
The thir step is matching of the words is scored by a given substitution
matri#. word is considered a match if it is above a threshold.
The fourth step involves pairwise alignment by e#tending from the words in
both directions while counting the alignment score using the same substitution
The e#tension continues until the score of the alignment drops below a threshold
due to mismatches 5the drop threshold is twenty1two for proteins and twenty for
The resulting contiguous aligned segment pair without gaps is called high!
scoring segment pair *$SP+
!n the original version of -.$T, the highest scored 7$8s are presented as the
final report. They are also called ma#imum scoring pairs.
!mprovement in the implementation of -.$T is the ability to provide
gapped alignment.
!n gapped -.$T, the highest scored segment is chosen to be e#tended in both
directions using dynamic programming where gaps may be introduced.
The e#tension continues if the alignment score is above a certain threshold.
-.$T is a family of programs that includes
-.$T2, queries nucleotide sequences with a nucleotide sequence
-.$T8, uses protein sequences as queries to search against a protein
sequence database.
-.$T9 uses nucleotide sequences as queries and translates them in all si#
reading frames to produce translated protein sequences, which are used to
query a protein sequence database.
T-.$T2, queries protein sequences to a nucleotide sequence database with
the sequences translated in all si# reading frames.
T-.$T9. uses nucleotide sequences, which are translated in all si# frames,
to search against a nucleotide sequence database that has all the sequences
translated in si# frames.

!n addition, there is also a bl,seq program that performs local alignment of two
user1provided input sequences.
The -.$Tweb$T:6
The graphical output includes horizontal bars and a diagonal in a two1dimensional
diagram showing the overall e#tent of matching between the two sequences..
The -.$T output provides a list of pairwise sequence matches ranked by
The significance scores help to distinguish evolutionarily related sequences from
unrelated ones.
;enerally, only hits above a certain threshold are displayed.
!n -.$T searches, this statistical indicator is known as the E1value 5e#pectation
and it indicates the probability that the resulting alignments from a database
are caused by random chance.
The E1value is related to the P1value used to assess significance of single
pairwise alignment.
-.$T compares a query sequence against all database sequences, and so the
E1value is determined by the following formula(
E < m = n = P
where m is the total number of residues in a database,
n is the number of residues in the query sequence, and
P is the probability that an 7$8 alignment is a result of random chance.
'g> +*?@. !t is e#pressed as +e % @ in -.$T output. This indicates that the
probability of this database sequence match occurring due to random chance is
TheE1value provides information about the likelihood that a given sequencematch
is purely by chance.
The lower the E1value, the less likely the database match is a result of random
chance and therefore the more significant the match is.
bit score is another prominent statistical indicator used in addition to the
in a -.$T output.
The bit score measures sequence similarity independent of query sequence
length and database size and is normalized based on the raw pairwise
alignment score. 5SA6
Thus, the higher the bit score, the more highly significant the match is.
B(AST )ut-ut .ormat
The-.$Tout puti ncludes a graphical overview bo#, a matching list and a te#t
description of the alignment.
The graphical overview bo# contains colored horizontal bars that allow quick
identification of the number of database hits and the degrees of similarity of the

The color coding of the horizontal bars corresponds to the ranking of similarities
of the sequence hits 5red( most related> green and blue( moderately related>
black( unrelated6.

The length of the bars represents the spans of sequence alignments relative to
the query sequence.
'ach bar is hyperlinked to the actual pairwise alignment in the te#t portion of the

The graphical bo# is a list of matching hits ranked by the E1values in ascending
order. 'ach hit includes the accession number, title 5usually partial6 of the
database record, bit score, and E1value.
This list is followed by the te#t description,which may be divided into threes
ections( the header, statistics, and alignment.

The header section contains the gene inde# number or the reference number of
the database hit plus a one1line description of the database sequence.
This is followed by the summary of the statistics of the search output, which
includes the bit score, E1value, percentages of identity, similarity 58ositives6, and
!n the actual alignment section, the query sequence is on the top of the pair and
the database sequence is at the bottom of the pair labeled as Subject.

!n between the two sequences, matching identical residues are written out at their
corresponding positions, where as nonidentical but similar residues are labeled
with B.

ny residues identified as .3Cs D5lowcomplexity regions )in the query sequence
are masked with Xs or Ns so that no alignment is represented in those regions.
D5/or both protein andD2 sequences, there may be regions that contain
highly repetitive residues, such as short segments of repeats, or segments that
are over represented by a small number of residues. 6
/$T 5/$T .., preceding the development of
-.$T ,/$T was in fact the first database similarity search tool developed.
/$T uses a hashing strategy to find matches for a short stretch of identical
residues with a length of k.
The string of residues is known as ktuples or ktups, which are equivalent to
words in
-.$T, but are normally shorter than the words.
Typically, a ktup is composed of two residues for protein sequences and si#
residues for D2 sequences.
The first ste- in /$T alignment is to identify ktups between two
sequences by
using the hashing strategy.
This strategy works by constructing a lookup table that shows the position of
each ktup for the two sequences under consideration.
The positional difference for each word between the two sequences is obtained
by subtracting the position of the first sequence from that of the second
sequence and is e#pressed as the offset.
The ktups that have the same offset values are then linked to reveal a
contiguous identical sequence region that corresponds to a stretch of diagonal in
a two1dimensional matri#.
The second ste- is to narrow down the high similarity regions between the
two sequences.
The top ten regions with the highest density of diagonals are identified as high
similarity regions.
The diagonals in these regions are scored using a substitution matri#.
2eighboring high1scoring segments along the same diagonal are selected and
0oined to form a single alignment.
This step allows introducing gaps between the diagonals while applying gap
penalties. The score of the gapped alignment is calculated again.
!n ste- /, the gapped alignment is refined further using the $mith%&aterman
algorithm to produce a final alignment
The last ste- is to perform a statistical evaluation of the final alignment as in
-.$T, which produces the E1value.
$imilar to -.$T, /$T has a number of subprograms.
The web1based /$T program offered by the 'uropean -ioinformatics !nstitute allows the use of either DNA or -rotein se0uences as the
0uery to search a#ainst a -rotein dataase or nucleotide dataase.
$ome available variants of the program are
.AST1, which trans"ates a DN#s e$uence and uses the trans"ate protein
se$uence to $uery a protein ata%ase, and
T.AST1, which compares a protein $uery se$uence to a trans"ate DN#
Statistical Si#nificance
/$T also uses E23alues and it scores.
7owever, the /$T output provides one more statistical parameter, the &2score.
This describes the numer of standard de3iations from the mean score for the
database search.
-ecause most of the alignments with the query sequence are with unrelated
sequences,the hi#her the &2score for a reported match, the further away from the
mean of the score distribution, hence, the more si#nificant the match.
Z1score E +F, e#tremely $ignificant.
F to +F, highly probable homologs.
Z G F, their relationships is described as less certain.
!n the dynamic programming algorithm presented, the alignment procedure has
make use of a scorin# system, which is a set of 3alues for 0uantifyin# the
li"elihood of
one residue ein# sustituted y another in an ali#nment .
The scoring systems is ca""e a su%stitution matrix and is deri3ed from
statistical analysis of residue sustitution data from sets of reliale
ali#nments of hi#hly related se0uences.
$coring matrices for nucleotide sequences are relatively simple. # positive
or high score is given for a match and a negative va"ue or "o' score for a
$coring matrices for amino acids are more complicated because scoring has to
reflect the physicochemical properties of amino acid residues, as well as the
of certain residues.
The hydrophobic residue group includes methionine, isoleucine, leucine, and
$mall and polar residues include serine, threonine, and cysteine.
Cesidues within these groups have high likelihoods of being substituted for each
7owever, cysteine contains a sulfhydryl #rou- that plays a role in metal
binding, active site, and disulfide bond formation.
Sustitution of cysteine 4ith other residues therefore often aolishes the
en5ymatic activity or destabilizes the protein structure.
mino acid substitution matrices, which are 67 8 67 matrices, have been
devised to
reflect the likelihood of residue substitutions.
There are essentially t4o ty-es of amino acid substitution matrices.

"ne type is based on interchangeability of the #enetic code or amino

acid -ro-erties, and

The other is derived from em-irical studies of amino acid substitutions.

lthough the two different approaches coincide to a certain e#tent, the first
approach considered as less accurate than the second approach.
The em-irical matrices, which include PAM and B()SUM matrices, are
derived from actual alignments of high"y simi"ar se$uences(
-y analyzing the probabilities of amino acid substitutions in these alignments, a
scoring system can be developed by giving a high score for a more likely
substitution and a low score for a rare substitution.
-ositi3e score represent substitutions of very similar residues or identical
9ero score means relationship between the amino acids is 4ea"ly similar at
best in terms of physicochemical properties.
ne#ati3e score means substitutions between dissimilar residues.
The sustitution matrices a--ly lo#arithmic con3ersions to describe the
of amino acid substitutions.
The con3erted 3alues are the so2called lo#2odds scores *or lo#2odds
*which are logarithmic ratios of the observed mutation frequency divided by the
probability of substitution e#pected by random chance6
The conversion can be either to the base of :7 or to the ase of 6.
/or e#ample, in an alignment that involves ten sequences, each having only one
aligned position, nine of the sequences are / 5phenylalanine6 and the remaining one
! 5isoleucine6.
The observed frequency of ! being substituted by / is one in ten 5*.+6
whereas the probability of ! being substituted by / by random chance is one in
twenty 5*.*F6.
Thus, the ratio of the two probabilities is , 5*.+:*.*F6.
fter taking this ratio to the logarithm to the base of ,, this makes the log odds equal
to +
This value can then be interpreted as the likelihood of substitution between the two
residues being , +.
which is two times more frequently than by random chance.
PAM B()SUMMatrices H
PAM Matrices
The 8I matrices 5also called Dayhoff PAM matrices6 were first constructed by
Iargaret Dayhoff, who com-iled ali#nments of se3enty2one #rou-s of 3ery
closely related -rotein se0uences.
8I stands for -oint acce-ted mutation 5although accepted point
mutation or 8I may be a more appropriate term, 8I is easier to pronounce6.
-ecause of the use of 3ery closely related homolo#s, the oser3ed
mutations 4ere
not e!-ected to si#nificantly chan#e the common function of the -roteins.
Thus, the observed amino acid mutations are considered to be accepted by
The PAM matrices were suse0uently deri3ed ased on the e3olutionary
di3er#ence et4een se0uences of the same cluster.
)ne PAM unit is defined as :; of the amino acid
-ositions that ha3e een chan#ed.
To construct a 8I+ substitution table, a group of closely related sequences with
mutation frequencies corresponding to one 8I unit is chosen.
-ased on the collected mutational data from this group of sequences, a substitution
matri# can be derived.
3onstruction of the 8I+ matri# involves alignment of full1length sequences and
subsequent construction of phylogenetic trees using the parsimony principle.
This allows computation of ancestral sequences for each internal node of the trees
ncestral sequence information is used to count the number of substitutions
along each branch of a tree.
The PAM score for a -articular residue -air is derived from a multiste-
-rocedure involving calculations of relative mutaility, normali5ation of the
e!-ected residue sustitution fre0uencies y random chance, and
lo#arithmic transformation to the ase of :7 of the normalized mutability value
di3ided y the fre0uency of a -articular residue.
The resulting value is rounded to the nearest integer and entered into the
substitution matri#, which reflects the likelihood of amino acid substitutions.
This completes the log1odds score computation.
fter compiling all substitution probabilities of possible amino acid mutations, a ,*
= ,* 8I matri# is established.
8ositive scores in the matri# denote substitutions occurring more frequently than
e#pected among evolutionarily conserved replacements. 2egative scores
correspond to substitutions that occur less frequently than e#pected.
"ther 8I matrices with increasing numbers for more divergent sequences are
e#trapolated from 8I+ through matri# multiplication.
/or e#ample, 8IJ* is produced by values of the 8I+ matri# multiplied by itself
eighty times.
8I unit is defined as +K amino acid change or one mutation per +** residues.
The increasing 8Inumbers correlate with increasing 8Iunits and thus
distances of protein sequences.
/or e#ample, 8I,F*, which corresponds to ,*K amino acid identity, represents
,F* mutations per +** residues.
!n theory, the number of evolutionary changes appro#imately corresponds to an
e#pected evolutionary span of ,,F** million years.
Thus, the 8I,F* matri# is normally used for divergent sequences.
ccordingly, 8I matrices with lower serial numbers are more suitable for
aligning more closely related sequences.
!n the 8I matri# construction, the only direct observation of residue substitutions
is in 8I+, based on a relatively small set of e#tremely closely related
$equence alignment statistics for more divergent sequences are not available.
To fill in the gap, a new set of substitution matrices have been developed.
This is the series of blocks amino acid substitution matrices 5-."$LI6, all of
which are derived based on direct observation for every possible amino acid
substitution in multiple sequence alignments .
These were constructed based on more than ,,*** conserved amino acid
patterns representing F** groups of protein sequences.
The sequence patterns, also called blocks, are un gapped alignments of less than
si#ty amino acid residues in length.
The frequencies of amino acid substitutions of the residues in these blocks are
calculated to produce a numerical table, or block substitution matri#.
!nstead of using the e#trapolation function, the -."$LI matrices are actual
identity values of sequences selected for construction of the matrices.
/or e#ample,-."$LI@,indicates that the sequencess elected for constructing the
matri# share an average identity value of @,K.
!n the reversing order as the 8I numbering system, the lower the -."$LI
number, the more divergent sequences they represent.
The -."$LI score for a particular residue pair is derived from the log ratio of
observed residue substitution frequency versus the e#pected probability of a
particular residue.
The log odds is taken to the base of , instead of +* as in the 8Imatrices.
The resulting value is rounded to the nearest integer and entered into the
positive and negative values correspond to substitutions that occur more or less
frequently than e#pected among evolutionarily conserved replacements.
PAM matrices B()SUM matrices
8I matrices, e#cept 8I+, are derived
from an evolutionary
8I matrices are used most often for
reconstructing phylogenetic
-."$LI matrices consist of entirely
direct observations
&ith the usage of mathematical
e#trapolation procedure,
8I values may be less realistic for
divergent sequences
-."$LI matrices are actual percentage
identity values
8I+ global alignment
local sequence alignments of conserved
sequence blocks
high 8I numbers are used to align
divergent sequences
lower the -."$LI number, the more
divergent sequences they represent
T$AN< =)U