Pairwise sequence alignments

Volker Flegel Vassilios Ioannidis

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Outline

Introduction Definitions Biological context of pairwise alignments Computing of pairwise alignments Some programs

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Importance of pairwise alignments

Sequence analysis tools depending on pairwise comparison
Multiple alignments Profile and HMM making (used to search for protein families and domains) 3D protein structure prediction Phylogenetic analysis Construction of certain substitution matrices Similarity searches in a database

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Goal
Sequence comparison through pairwise alignments
Goal of pairwise comparison is to find conserved regions (if any) between two sequences Extrapolate information about our sequence using the known characteristics of the other sequence
THIO_EMENI THIO_EMENI ??? ??? GFVVVDCFATWCGPCKAIAPTVEKFAQTY GFVVVDCFATWCGPCKAIAPTVEKFAQTY G G ++VD ++VD +A +A WCGPCK WCGPCK IAP IAP +++ +++ A A Y Y GAILVDFWAEWCGPCKMIAPILDEIADEY GAILVDFWAEWCGPCKMIAPILDEIADEY

Extrapolate Extrapolate

???

THIO_EMENI

SwissProt

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Do alignments make sense ?

Evolution of sequences
Sequences evolve through mutation and selection ! Selective pressure is different for each residue position in a protein (i.e. conservation of active site, structure, charge, etc.) Modular nature of proteins ! Nature keeps re-using domains Alignments try to tell the evolutionnary story of the proteins

Relationships
Same Sequence

Same Origin

Same Function

Same 3D Fold

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Example: An alignment

- textual view

Two similar regions of the Drosophila melanogaster Slit and Notch proteins

970 980 990 1000 1010 1020 970 980 990 1000 1010 1020 SLIT_DROME FSCQCAPGYTGARCETNIDDCLGEIKCQNNATCIDGVESYKCECQPGFSGEFCDTKIQFC SLIT_DROME FSCQCAPGYTGARCETNIDDCLGEIKCQNNATCIDGVESYKCECQPGFSGEFCDTKIQFC ..:.: :. :.: ...:.: .. : :.. : ::.. . :.: ::..:. :. :. : ..:.: :. :.: ...:.: .. : :.. : ::.. . :.: ::..:. :. :. : NOTC_DROME YKCECPRGFYDAHCLSDVDECASN-PCVNEGRCEDGINEFICHCPPGYTGKRCELDIDEC NOTC_DROME YKCECPRGFYDAHCLSDVDECASN-PCVNEGRCEDGINEFICHCPPGYTGKRCELDIDEC 740 750 760 770 780 790 740 750 760 770 780 790

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Example: An alignment

- graphical view

Comparing the tissue-type and urokinase type plasminogen activators. Displayed using a diagonal plot or Dotplot.
Tissue-Type plasminogen Activator Urokinase-Type plasminogen Activator URL: www.isrec.isb-sib.ch/java/dotlet/Dotlet.html

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Some definitions
Identity Proportion of pairs of identical residues between two aligned sequences. Generally expressed as a percentage. This value strongly depends on how the two sequences are aligned. Similarity Proportion of pairs of similar residues between two aligned sequences. If two residues are similar is determined by a substitution matrix. This value also depends strongly on how the two sequences are aligned, as well as on the substitution matrix used. Homology Two sequences are homologous if and only if they have a common ancestor. There is no such thing as a level of homology ! (It's either yes or no)
Homologous sequences do not necessarily serve the same function... ... Nor are they always highly similar: structure may be conserved while sequence is not.

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More definitions
Consider a set S (say, globins) and a test t that tries to detect members of S (for example, through a pairwise comparison with another globin).

True positive
A protein is a true positive if it belongs to S and is detected by t.

True negative
A protein is a true negative if it does not belong to S and is not detected by t.

False positive
A protein is a false positive if it does not belong to S and is (incorrectly) detected by t.

False negative
A protein is a false negative if it belongs to S and is not detected by t (but should be).

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Definition example
The set of all globins and a test to identify them
Consider: a set S (say, globins: G) a test t that tries to detect members of S
(for example, through a pairwise comparison with another globin). Globins

G
True positives True negatives False positives False negatives Matches VI - 2004

G G G G
X

G
X X X
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Even more definitions

Sensitivity
Ability of a method to detect positives, irrespective of how many false positives are reported.

Selectivity
Ability of a method to reject negatives, irrespective of how many false negatives are rejected.

Greater sensitivity Less selectivity True positives True negatives False positives False negatives VI - 2004 Page 11 Less sensitivity Greater selectivity

Pairwise sequence alignment

Concept of a sequence alignment
Pairwise Alignment: ! Explicit mapping between the residues of 2 sequences
deletion

Seq Seq A AGARFIELDTHELASTFA-TCAT GARFIELDTHELASTFA-TCAT ||||||||||| || ||||||||||| || |||| |||| Seq B GARFIELDTHEVERYFASTCAT Seq B GARFIELDTHEVERYFASTCAT
errors / mismatches insertion

Tolerant to errors (mismatches, insertion / deletions or indels) Evaluation of the alignment in a biological concept (significance)

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Pairwise sequence alignement

Number of alignments
There are many ways to align two sequences Consider the sequence fragments below: a simple alignment shows some conserved portions
CGATGCAGACGTCA CGATGCAGACGTCA |||||||| |||||||| CGATGCAAGACGTCA CGATGCAAGACGTCA

but also:
CGATGCAGACGTCA CGATGCAGACGTCA |||||||| |||||||| CGATGCAAGACGTCA CGATGCAAGACGTCA
Number of possible alignments for 2 sequences of length 1000 residues:

! more than 10600 gapped alignments

(Avogadro 1024, estimated number of atoms in the universe 1080)

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Alignement evaluation
What is a good alignment ?
We need a way to evaluate the biological meaning of a given alignment Intuitively we "know" that the following alignment:
CGAGGCACAACGTCA CGAGGCACAACGTCA ||| ||| ||| ||| |||||| |||||| CGATGCAAGACGTCA CGATGCAAGACGTCA

is better than:
ATTGGACAGCAATCAGG ATTGGACAGCAATCAGG | || | | || | | | ACGATGCAAGACGTCAG ACGATGCAAGACGTCAG

We can express this notion more rigorously, by using a scoring system

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Scoring system
Simple alignment scores
A simple way (but not the best) to score an alignment is to count 1 for each match and 0 for each mismatch.

CGAGGCACAACGTCA CGAGGCACAACGTCA ||| ||| ||| ||| |||||| |||||| CGATGCAAGACGTCA CGATGCAAGACGTCA

!Score: 12
ATTGGACAGCAATCAGG ATTGGACAGCAATCAGG | || | | || | | | ACGATGCAAGACGTCAG ACGATGCAAGACGTCAG

!Score: 5

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Introducing biological information

Importance of the scoring system !discrimination of significant biological alignments
Based on physico-chemical properties of amino-acids ! Hydrophobicity, acid / base, sterical properties, ... ! Scoring system scales are arbitrary Based on biological sequence information ! Substitutions observed in structural or evolutionary alignments of well studied protein families ! Scoring systems have a probabilistic foundation

Substitution matrices
In proteins some mismatches are more acceptable than others Substitution matrices give a score for each substitution of one aminoacid by another

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Substitution matrices
Example matrix
(Leu, Ile): 2 (Leu, Cys): -6 ...

(log-odds matrices)

For a set of well known proteins:

Align the sequences Count the mutations at each position For each substitution set the score to the log-odd ratio

& # observed log$ $ expected by chance ! ! % "

Positive score: the amino acids are similar, mutations from one into the other occur
more often then expected by chance during evolution

Negative score: the amino acids are dissimilar, the mutation from one into the other
occurs less often then expected by chance during evolution

PAM250
From: A. D. Baxevanis, "Bioinformatics"

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Matrix choice
Different kind of matrices
PAM series (Dayhoff M., 1968, 1972, 1978)
Percent Accepted Mutation. A unit introduced by Dayhoff et al. to quantify the amount of evolutionary change in a protein sequence. 1.0 PAM unit, is the amount of evolution which will change, on average, 1% of amino acids in a protein sequence. A PAM(x) substitution matrix is a look-up table in which scores for each amino acid substitution have been calculated based on the frequency of that substitution in closely related proteins that have experienced a certain amount (x) of evolutionary divergence.

! Based on 1572 protein sequences from 71 families ! Old standard matrix: PAM250

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Matrix choice
Different kind of matrices
BLOSUM series (Henikoff S. & Henikoff JG., PNAS, 1992)
Blocks Substitution Matrix. A substitution matrix in which scores for each position are derived from observations of the frequencies of substitutions in blocks of local alignments in related proteins. Each matrix is tailored to a particular evolutionary distance. In the BLOSUM62 matrix, for example, the alignment from which scores were derived was created using sequences sharing no more than 62% identity. Sequences more identical than 62% are represented by a single sequence in the alignment so as to avoid over-weighting closely related family members.

! Based on alignments in the BLOCKS database ! Standard matrix: BLOSUM62

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Matrix choice
Limitations
Substitution matrices do not take into account long range interactions between residues. They assume that identical residues are equal (whereas in reallife a residue at the active site has other evolutionary constraints than the same residue outside of the active site) They assume evolution rate to be constant.

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Alignment score
Amino acid substitution matrices
Example: Most used: PAM250 Blosum62

Raw score of an alignment

TPEA TPEA _| _| | | APGA APGA

Score = 1 + 6 + 0 + 2 = 9

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Gaps
Insertions or deletions
Proteins often contain regions where residues have been inserted or deleted during evolution There are constraints on where these insertions and deletions can happen (between structural or functional elements like: alpha helices, active site, etc.)

Gaps in alignments
GCATGCATGCAACTGCAT GCATGCATGCAACTGCAT ||||||||| ||||||||| GCATGCATGGGCAACTGCAT GCATGCATGGGCAACTGCAT

can be improved by inserting a gap

GCATGCATG--CAACTGCAT GCATGCATG--CAACTGCAT ||||||||| ||||||||| ||||||||| ||||||||| GCATGCATGGGCAACTGCAT GCATGCATGGGCAACTGCAT
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Gap opening and extension penalties

Costs of gaps in alignments
We want to simulate as closely as possible the evolutionary mechanisms involved in gap occurence.

Example
Two alignments with identical number of gaps but very different gap distribution. We may prefer one large gap to several small ones
(e.g. poorly conserved loops between well-conserved helices)

CGATGCAGCAGCAGCATCG CGATGCAGCAGCAGCATCG |||||| ||||||| |||||| ||||||| CGATGC------AGCATCG CGATGC------AGCATCG

gap opening gap extension

CGATGCAGCAGCAGCATCG CGATGCAGCAGCAGCATCG || || || || |||| |||| || || || || | | CG-TG-AGCA-CA--AT-G CG-TG-AGCA-CA--AT-G

Gap opening penalty

Counted each time a gap is opened in an alignment
(some programs include the first extension into this penalty)

Gap extension penalty

Counted for each extension of a gap in an alignment
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Gap opening and extension penalties

Example
With a match score of 1 and a mismatch score of 0 With an opening penalty of 10 and extension penalty of 1, we have the following score:

CGATGCAGCAGCAGCATCG CGATGCAGCAGCAGCATCG |||||| ||||||| |||||| ||||||| CGATGC------AGCATCG CGATGC------AGCATCG

gap opening gap extension

CGATGCAGCAGCAGCATCG CGATGCAGCAGCAGCATCG || || || || |||| |||| || || || || | | CG-TG-AGCA-CA--AT-G CG-TG-AGCA-CA--AT-G

13 x 1 - 10 - 6 x 1 = -3

13 x 1 - 5 x 10 - 6 x 1 = -43

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Statistical evaluation of results

Alignments are evaluated according to their score
Raw score ! It's the sum of the amino acid substitution scores and gap penalties (gap opening and gap extension) ! Depends on the scoring system (substitution matrix, etc.) ! Different alignments should not be compared based only on the raw score
It is possible that a "bad" long alignment gets a better raw score than a very good short alignment. ! We need a normalised score to compare alignments ! ! We need to evaluate the biological meaning of the score (p-value, e-value).

Normalised score ! Is independent of the scoring system ! Allows the comparison of different alignments ! Units: expressed in bits

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Statistical evaluation of results

Distribution of alignment scores - Extreme Value Distribution
Random sequences and alignment scores ! Sequence alignment scores between random sequences are distributed following an extreme value distribution (EVD).

Random sequences Ala Ala Val Val ... ... Tr p Tr p

Pairwise alignments

Score distribution

...

...

score y score

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obs

score x

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Statistical evaluation of results

Distribution of alignment scores - Extreme Value Distribution
High scoring random alignments have a low probability. The EVD allows us to compute the probability with which our biological alignment could be due to randomness (to chance). Caveat: finding the threshold of significant alignments.

Threshold significant alignment

score
score x: our alignment has a great probability of being the result of random sequence similarity score y: our alignment is very improbable to obtain with random sequences

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Statistical evaluation of results

Statistics derived from the scores
100%

0% N

p-value ! Probability that an alignment with this score occurs by chance in a database of this size ! The closer the p-value is towards 0, the better the alignment e-value ! Number of matches with this score one can expect to find by chance in a database of this size ! The closer the e-value is towards 0, the better the alignment Relationship between e-value and p-value: ! In a database containing N sequences e=pxN

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Diagonal plots or Dotplot

Concept of a Dotplot
Produces a graphical representation of similarity regions. The horizontal and vertical dimensions correspond to the compared sequences. A region of similarity stands out as a diagonal.
Tissue-Type plasminogen Activator Urokinase-Type plasminogen Activator

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Dotplot construction
Simple example
A dot is placed at each position where two residues match. ! The colour of the dot can be chosen according to the substitution value in the substitution matrix
THEFATCATTHEFASTCAT

THEFA-TCAT THEFA-TCAT ||||| ||||| |||| |||| THEFASTCAT THEFASTCAT

Note
This method produces dotplots with too much noise to be useful ! The noise can be reduced by calculating a score using a window of residues ! The score is compared to a threshold or stringency
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Dotplot construction
Window example
Each window of the first sequence is aligned (without gaps) to each window of the 2nd sequence A colour is set into a rectangular array according to the score of the aligned windows
THEFATCATTHEFASTCAT

THE HEF THE CAT HEF THE CAT ||| ||| THE HEF THE THE HEF
-5 Score: 23 -4

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Dotplot limitations
! It's a visual aid.
The human eye can rapidly identify similar regions in sequences. ! It's a good way to explore sequence organisation. ! It does not provide an alignment.
Tissue-Type plasminogen Activator Urokinase-Type plasminogen Activator

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Creating an alignment
Relationship between alignment and dotplot
An alignment can be seen as a path through the dotplot diagramm.

Seq B SeqB B B Seq A SeqA A A VI - 2004

ACA--CA A-CA-CA ACA--CA A-CA-CA || || || || A-CCAAC ACCAACA-CCAAC ACCAACPage 33

Finding an alignment
Alignment algorithms
An alignment program tries to find the best alignment between two sequences given the scoring system.
This can be seen as trying to find a path through the dotplot diagram including all (or the most visible) diagonals.

Alignement types
Global Local Alignment between the complete sequence A and the complete sequence B Alignment between a sub-sequence of A an a subsequence of B

Computer implementation (Algorithms)

Dynamic programing Global Needleman-Wunsch Local Smith-Waterman

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Global alignment

(Needleman-Wunsch)

Example ! Global alignments are very sensitive to gap penalties ! Global alignments do not take into account the modular nature of
proteins
Urokinase-Type plasminogen Activator Tissue-Type plasminogen Activator

Global alignment:

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Local alignment
proteins

(Smith-Waterman)

Example ! Local alignments are more sensitive to the modular nature of ! They can be used to search databases
Tissue-Type plasminogen Activator Urokinase-Type plasminogen Activator

Local alignments: VI - 2004 Page 36

Optimal alignment extension

How to extend optimaly an optimal alignment An optimal alignment up to positions i and j can be extended in 3 ways. Keeping the best of the 3 guarantees an extended optimal alignment. Seq Seq A A Seq Seq B B Seq Seq A A Seq Seq B B Seq Seq A A Seq Seq B B Seq Seq A A Seq Seq B B a a2 a ... a i-1 a a1 a3 ai 1 a2 3 ... ai-1 i b b2 b ... b j-1 b b1 b3 bj 1 b2 3 ... bj-1 j a a2 a ... a i-1 a a1 a3 ai 1 a2 3 ... ai-1 i b b2 b ... b j-1 b b1 b3 bj 1 b2 3 ... bj-1 j a a2 a ... a i-1 a a1 a3 ai 1 a2 3 ... ai-1 i b b2 b ... b j-1 b b1 b3 bj 1 b2 3 ... bj-1 j a a2 a ... a i-1 a a1 a3 ai 1 a2 3 ... ai-1 i b b2 b ... b j-1 b b1 b3 bj 1 b2 3 ... bj-1 j a ai+1 i+1 b bj+1 j+1 a ai+1 i+1 b bj+1 j+1
Score = Scoreij - gap Score = Scoreij - gap Score = Scoreij + Substi+1j+1

We have the optimal alignment extended from i and j by one residue.

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Exact algorithms
Simple example (Needleman-Wunsch)
Scoring system:
F(i-1,j2 -1 -2
1) s(xi,yj)

F(i,j1)

! Match score: ! Mismatch score: ! Gap penalty:

-d

F(i1,j)

-d

F(i,j)

i j 0-2-4-6-8-10 -2 -10A 0-2-4-6-8-10 0-2-4-6-8-10 -220-2-4-6 -220-2-4-6 -404 -40420-2 -6T -8 -6-22312 GATTA G A-4A-6T-8 C-12 GATTA GATTA G G AT A T-10 C-12 T-8-40453 T-10-6-2264 C-12-8-4045 value) for residues x and y

F(i,j): score at position i, j s(x ,y ): match or mismatch score (or substitution matrix d: gap penalty (positive value)
i j

2+2

0-2

0-2

Note

GA-TTA GA-TTA || || || || GAATTC GAATTC

We have to keep track of the origin of the score for each element in the matrix. ! This allows to build the alignment by traceback when the matrix has
been completely filled out.

Computation time is proportional to the size of sequences (n x m).

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Algorithms for pairwise alignments

Web resources
LALIGN - pairwise sequence alignment:
www.ch.embnet.org/software/LALIGN_form.html

PRSS - alignment score evaluation:

www.ch.embnet.org/software/PRSS_form.html

Concluding remarks
Substitution matrices and gap penalties introduce biological information into the alignment algorithms. It is not because two sequences can be aligned that they share a common biological history. The relevance of the alignment must be assessed with a statistical score. There are many ways to align two sequences.
Do not blindly trust your alignment to be the only truth. Especially gapped regions may be quite variable.

Sequences sharing less than 20% similarity are difficult to align: ! You enter the Twilight Zone (Doolittle, 1986) ! Alignments may appear plausible to the eye but are no longer ! Other methods are needed to explore these sequences (i.e:
profiles)
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statistically significant.