Multiple Sequence Alignment

1. Multiple Sequence Alignment Sushmita Roy BMI/CS 576 www.biostat.wisc.edu/bmi576/ sroy@biostat.wisc.edu Sep 18th, 2014

2. Key concepts • The Multiple Sequence Alignment Problem • Scoring Multiple Sequence Alignments • Scoring an alignment of a “profile” and a sequence • Heuristic Algorithms for Multiple Sequence Alignment • General strategies • Progressive alignment • Star alignment • Tree-based alignment • Iterative alignment • Understanding of key steps in common algorithms • Progressive: CLUSTAL • Iterative: MUSCLE

3. Readings • Durbin Chapter 6 • 6.1 • 6.2 • 6.3: ClustalW • 6.4 • CLUSTALW • MUSCLE

4. What is multiple sequence alignment? The task of locating equivalent regions of more than two sequences so as to maximize their overall similarity.

5. Why multiple sequence alignment? • Build phylogenetic trees (next module) • Determine evolutionary relationships between sequences • A multiple sequence alignment can represent a family of proteins with similar function • Compare new sequence to a “family” of known proteins • For example the BLOCKS database used for BLOSUM contains several ungapped alignments for known protein families • Discover common signatures or protein domains among a group of proteins • Identify genetic variation among individuals of a population

6. An example multiple sequence alignment

7. The tasks in Multiple Sequence Alignment • Scoring an alignment • Algorithms for creating an alignment

8. Some notation • Let m denote a Multiple Sequence Alignment • mi is the ith column of the alignment m • mij is the ith column and jth row • cia count of residue a in column i

9. Example using notation G A R F I E L D T H E F A T C A T G A R F I E L D T H E _ _ _ C A T G A R F I E L D T H A T _ _ C A T G A R R Y _ L I K E D A _ _ C A T

10. Scoring a Multiple Sequence Alignment (MSA) • Key issue: how do we score a multiple sequence alignment? • Usually, we assume thatcolumnsof an alignment are independent • We will simplify score by assuming linear gap penalty for now as gap function score of ith column

11. Gap penalty (G) • We will use a simple linear gap penalty function • Penalty for a gap: g • Let s(a,b) denote the cost of substitutinga byb. • Linear gap penalty can be incorporated into the substitution matrix • s(a,_)=-g=s(_,a) • s(_,_)=0

12. Two ways to score are used • Entropy based scores • Sum of pairs

13. Entropy of a distribution • A measure of average uncertainty of an outcome • For a discrete distribution P(X), where X takes k values x1, .. xk it is defined as • Entropy is greatest when we are most uncertain, that is, for a uniform distribution • Entropy is least when we are most certain, e.g. deterministic event

14. Score of a column: Entropy based • Score of the ith column of alignment m is • This has an entropy-based interpretation • First, the probability of a column mi • Second, taking log on both sides and putting a “-” sign gives us the entropy-based score

15. Scoring an alignment: Entropy based score • Taking log on both sides and putting a “-” sign gives us the entropy-based score • This looks similar to entropy of a random variable specifying the character a in this column. • High entropy: More uniform distribution/more variability of characters • Low entropy: Less uniform distribution/less variability of characters

16. Scoring of a column: Sum of Pairs • Compute the sum of the pairwise scores Iterate over all pairs of rows in the column Substitution score from a substitution/match matrix such as BLOSUM or PAM

17. Algorithms for performing a Multiple Sequence Alignment • Dynamic programming • Not feasible • Progressive alignment algorithms • Star alignment • Guide tree approach • Iterative alignment algorithms

18. Dynamic Programming (DP) for multiple sequence alignment • Assume columns are independent • Score of alignment is sum of scores per column • Generalization of methods for pairwise alignment • consider k-dimensional matrix for k sequences (instead of 2-dimensional matrix) • each matrix element represents alignment score for k subsequences (instead of 2 subsequences)

19. Notation for DP • Assume we have k sequences • i1 denotes where we are in the sequence 1 • i2 denotes where we are in sequence 2 • … • ikdenotes where we are in sequencek • denotes the character at ik position of sequence xk • F: k-dimensional matrix where denotes the score of the best partial alignment uptoi1, i2.. ik parts of the sequences

20. Recall the DP for the pairwise alignment

21. DP for Multiple sequence alignment max score of alignment for the k subsequences How many items do we need to maximize over? 2k -1

22. DP algorithm is too expensive • For k sequences each of length n • Space complexity: O(nk) • Time complexity: O(nk2k)

23. Heuristic algorithms to Multiple sequence alignment • Progressive alignment • Build the alignment of larger number of sequences from partial alignments of subsets of sequences • Iterative alignment • Possibly remove some of the aligned sequences and re-align to see if score improves

24. Progressive alignment • Key heuristic: Align the “most similar” sequences first • Rely on pre-computed pairwise similarity/distance • Pairwise sequence alignments • Algorithms differ in the extent to which the pairwise similarity influences the final alignments • Two strategies • Star alignment • Tree alignments • Simple (quick and dirty) tree • At each time combine two, possibly singleton, sets of sequences

25. Star Alignment Approach • Given: k sequences to be aligned • pick one sequence as the “center” • for each determine an optimal alignment between and • Aggregate pairwise alignments • Shift entire columns when incorporating gaps • return: multiple alignment resulting from aggregate

26. Picking the center in star alignments Two possible approaches: • try each sequence as the center, return the best multiple alignment • compute all pairwise alignments and select the string that maximizes:

27. Aligning to an existing partial alignment • Need to treat each “partial alignment” as a single entity • Partial alignment should not be changed other than gap insertions • Shift entire columns when incorporating gaps TGTTAAC -TGTTAAC -TGT-AAC -TGT--AC ATGT---C ATGT-GGC -TGT AAC -TGT -AC ATGT --C ATGT GGC

28. Star Alignment Example Given: ATGGCCATT ATTGCCATT ATTGCCATT ATGGCCATT ATCCAATTTT ATC-CAATTTT ATTGCCATT-- ATCTTCTT ATTGCCGATT ATTGCCATT ATTGCCGATT ATTGCC-ATT ATCTTC-TT ATTGCCATT

29. Star Alignment Example • Aggegate pairwise alignments present pair Current multiple alignment ATGGCCATT ATTGCCATT ATTGCCATT ATGGCCATT 1. ATC-CAATTTT ATTGCCATT-- ATTGCCATT-- ATGGCCATT-- ATC-CAATTTT 2.

30. Star Alignment Example present pair Current multiple alignment ATCTTC-TT ATTGCCATT ATTGCCATT-- ATGGCCATT-- ATC-CAATTTT ATCTTC-TT-- 3. ATTGCCGATT ATTGCC-ATT ATTGCC- A TT-- ATGGCC- A TT-- ATC-CA- A TTTT ATCTTC- - TT-- ATTGCCG A TT-- 4. shift entire columns when incorporating a gap

31. Comments about Star alignment • Conceptually simple • Dependent only upon pairwise alignments • Does not consider any position-specific information of the partial multiple sequence alignment while aligning a new sequence to it

32. Tree-based progressive alignments • Align sequences according to a guide tree • leaves represent sequences • internal nodes represent alignments • Determine alignments from bottom of tree upward • return multiple alignment represented at the root of the tree • One common variant: the CLUSTALW algorithm [Thompson et al. 1994]

33. Calculating the pairwise distance • Distance from Feng & Doolittle’s algorithm • Percent identity • For two sequences with the following alignment AATAATA ATAA_TA • Similarity S • No. of identical bases/size of alignment • 4/7 for the above example • Distance=1-S

34. Tree-based progressive alignment • Depending on the internal node in the tree, we may have to align a • a sequence with a sequence • a sequence with a partial alignment • a partial alignmentwith a partial alignment • In all cases we have the option of inserting gaps or substitutions • For aligning alignments, we will use sum of pairs scoring • To choose between options we will use an idea similar to the pairwise sequence alignment case

35. Tree alignment example • Starting sequences • Create a guide tree • Using pairwise distances (we will cover this in subsequent lectures) • Approach similar to but simpler than phylogenetic trees TGTTAAC TGTAAC TGTAC ATGTC ATGTGGC

36. Tree Alignment Example TGTAAC TGT-AC TGTTAAC TGTAAC TGTAC ATGTC ATGTGGC

37. Tree Alignment Example TGTAAC TGT-AC ATGT--C ATGTGGC TGTTAAC TGTAAC TGTAC ATGTC ATGTGGC

38. Tree Alignment Example Aligning two alignments -TGTAAC -TGT-AC ATGT--C ATGTGGC TGTAAC TGT-AC ATGT--C ATGTGGC TGTTAAC TGTAAC TGTAC ATGTC ATGTGGC

39. Tree Alignment Example -TGTTAAC -TGT-AAC -TGT--AC ATGT---C ATGT-GGC Aligning sequence to alignment -TGTAAC -TGT-AC ATGT--C ATGTGGC TGTAAC TGT-AC ATGT--C ATGTGGC TGTTAAC TGTAAC TGTAC ATGTC ATGTGGC

40. Scoring an alignment of partial alignments • Recall the sum of pairs score for a column i • Let 1 to n represent sequences from the first alignment • Let n+1 to N represent sequences from the second alignment, N denotes total number of sequences • Alignment at column ican be written as Within first alignment Within second alignment Between two alignments

41. Computing the sum of scores for two alignments • Assume we have two alignments corresponding to intermediate nodes of the guide tree • At each step we maximize over score from • aligning column i in A1 to a column j in A2 • aligning column i in A1 to gaps in A2 • aligning column j in A2 to gaps in A1 • ClustalW uses an average of all pairwise comparisons between two alignments Alignment A1 Alignment A2 AAAC_GAC AGCACC

42. ClustalW scores for aligning columns from two alignments Assume a score of 1 for mismatch, 2 for match and 0 for gap Score of aligning column 3 from Alignment 1 and column 2 from alignment 2 AAAC_GAC Alignment 1 Alignment 2 AGCACC

43. An example for aligning two alignments A A A C_ G A C A G CA C C Max of three options A _ A _ _ _ Alignment 1 A A _ _ A A Alignment 2

44. Comments about tree-based progressive alignment • Exploits partial alignment information • But, greedy • The tree might not be correct, that is, reflect an incorrect ordering of how sequences should be stacked up in the alignment • Final results prone to errors in alignment • Some positions might be misaligned (that is have a lower score than if a different ordering is used).

45. Additional notes about the ClustalW algorithm • Tailored to handle very divergent sequences: 25-30% similarity • Dynamically varies the gap penalties in a position and residue specific manner • Weight different sequences differently • Closely related sequences need to be down-weighted • Divergent sequences are up-weighted • Dynamically switch between substitution matrices depending upon the average similarity between sequences being aligned

46. Applying ClustalW to SH3 domain proteins Proteins share <12% sequence identity Alignment blocks correspond to beta strand secondary structures Thomson et al, 1994

47. Iterative refinement methods • The order of selection of sequences can influence the alignment • ClustalW overcomes some of these issues but has many heuristics and parameters • How to avoid committing to a non-optimal pairwise decision? • Revisit alignments • This is the focus of iterative alignments

48. Summary • Multiple sequence alignment is the problem of finding equivalent regions among more than two sequences • Scoring function: • Entropy based • Sum of pairs • Algorithms • Progressive • Star • Dependent upon a center • Keep adding all pairs of aligned sequences with the current alignment • Tree • Create an approximate guide tree • Use tree to align the sequences • Iterative • Don’t commit to the fixed ordering, revisit the alignment until score does not change

49. Slide Errata/Update • Slide 40 had a typo in the second equation • Slide 43 now has back arrows

50. Ordering matters Consider aligning GG, DGG and DGD 2 1 D G D _ G G D G D G G _ Are as good. But when we include DGG 2 1 D G D _ G G D G G D G D G G _ D G G 1 is better than 2, assuming a match score of 2, mismatch score =1, gap penalty=-2