The Smith Waterman algorithm
- 1. The Smith-Waterman algorithm Dr Avril Coghlan [email protected] Note: this talk contains animations which can only be seen by downloading and using ‘View Slide show’ in Powerpoint
- 2. Global versus Local Alignment • A global alignment covers the entire lengths of the sequences involved The Needleman-Wunsch algorithm finds the best global alignment between 2 sequences • A local alignment only covers parts of the sequences The Smith-Waterman algorithm finds the best local alignment between 2 sequences Global alignment Q K E S G P S S S Y C | | | | | V Q Q E S G L V R T T C Local alignment E S G | | | E S G
- 3. Local alignment • The concept of ‘local alignment’ was introduced by Smith & Waterman in 1981 • A local alignment of 2 sequences is an alignment between parts of the 2 sequences Two proteins may one share one stretch of high sequence similarity, but be very dissimilar outside that region A global (N-W) alignment of such sequences would have: (i) lots of matches in the region of high sequence similarity (ii) lots of mismatches & gaps (insertions/deletions) outside the region of similarity It makes sense to find the best local alignment instead
- 4. Real data: fruitfly & human Eyeless • This is a global alignment of human & fruitfly Eyeless Do you think it’s sensible to make a global alignment of these two sequences?
- 5. Real data: fruitfly & human Eyeless There are 2 short regions of high similarity Outside those regions, there are many mismatches and gaps It might be more sensible to make local alignments of one or both of the regions of high similarity
- 6. Real data: fruitfly & human Eyeless • This is a local alignment of human & fruitfly Eyeless What parts of the sequences were used in the local alignment?
- 7. The Smith-Waterman algorithm • S-W is mathematically proven to find the best (highest-scoring) local alignment of 2 sequences The best local alignment is the best alignment of all possible subsequences (parts) of sequences S1 and S2 The 0th row and 0th column of T are first filled with zeroes The recurrence relation used to fill table T is: T(i-1, j-1) + σ(S1(i), S2(j)) T(i, j) = max T(i-1, j) + gap penalty T(i, j-1) + gap penalty A 4th possibility (unlike 0 N-W) The traceback starts at the highest scoring cell in the matrix T, and travels up/left while the score is still positive (While in N-W, traceback starts at the bottom right, & ends at the top left, which ensures it’s a global alignment)
- 8. • eg., to find the best local alignment of sequences “ACCTAAGG” and “GGCTCAATCA”, using +2 for a match, -1 for a mismatch, and -2 for a gap: We first make matrix T (as in N-W): The 0th row and 0th column of T are filled with zeroes The recurrence relation is then used to fill the matrix T G G C T C A A T C A 0 0 0 0 0 0 0 0 0 0 0 A 0 C 0 C 0 T 0 A 0 A 0 G 0 G 0
- 9. We first calculate T(1,1) using the recurrence relation: T(i-1, j-1) + σ(S1(i), S2(j)) = 0 – 1 = -1 T(i, j) = max T(i-1, j) + gap penalty = 0 -2 = -2 T(i, j-1) + gap penalty = 0 -2 = -2 0 The maximum value is 0, so we set T(1,1) to 0 G G C T C A A T C A 0 0 0 0 0 0 0 0 0 0 0 We next calculate T(2,1)… A 0 0 ? ? C 0 C 0 T 0 A 0 A 0 G 0 G 0
- 10. You fill in the whole of T, recording the previous cell (if any) used to calculate the value of each T(i, j): G G G G C C T T C C A A A A T T C C A A 0 0 0 0 0 0 0 0 0 0 0 A 0 0 0 0 0 0 2 2 0 0 2 C 0 0 0 2 0 2 0 1 1 2 0 C 0 0 0 2 1 2 1 0 0 3 1 T 0 0 0 0 4 2 1 0 2 1 2 A A 0 0 0 0 2 3 4 3 1 1 3 A A 0 0 0 0 0 1 5 6 4 2 3 G G 0 2 2 0 0 0 3 4 5 3 1 G G 0 2 4 2 0 0 1 2 3 4 2
- 11. G G C T C A A T C A 0 0 0 0 0 0 0 0 0 0 0 A 0 0 0 0 0 0 2 2 0 0 2 C 0 0 0 2 0 2 0 1 1 2 0 C 0 0 0 2 1 2 1 0 0 3 1 T 0 0 0 0 4 2 1 0 2 1 2 A 0 0 0 0 2 3 4 3 1 1 3 A 0 0 0 0 0 1 5 6 4 2 3 G 0 2 2 0 0 0 3 4 5 3 1 G 0 2 4 2 0 0 1 2 3 4 2 You work out the best local alignment from the traceback (just like in N- W): C T C A A | | | | C T - A A
- 12. Software for making alignments • For Smith-Waterman pairwise alignment pairwiseAlignment() in the “Biostrings” R library the EMBOSS (emboss.sourceforge.net/) water program
- 13. Problem • Find the best local alignment between “TCAGTTGCC” & “AGGTTG”, with +1 for a match, -2 for a mismatch, and -2 for a gap.
- 14. Answer • Find the best local alignment between “TCAGTTGCC” & “AGGTTG”, with +1 for a match, -2 for a mismatch, and -2 for a gap Matrix T looks like this, with the pink traceback: T C A G T T G C C 0 0 0 0 0 0 0 0 0 0 A 0 0 0 1 0 0 0 0 0 0 Alignment: G 0 0 0 0 2 0 0 1 0 0 G T T G G 0 0 0 0 1 0 0 1 0 0 | | | | T 0 1 0 0 0 2 1 0 0 0 G T T G T 0 1 0 0 0 1 3 1 0 0 (Pink traceback) G 0 0 0 0 1 0 1 4 2 0
- 15. Further Reading • Chapter 3 in Introduction to Computational Genomics Cristianini & Hahn • Chapter 6 in Deonier et al Computational Genome Analysis • Practical on pairwise alignment in R in the Little Book of R for Bioinformatics: https://a-little-book-of-r-for- bioinformatics.readthedocs.org/en/latest/src/chapter4.html
Editor's Notes
- #4: Image credit (Temple Smith): http://www.modulargenetics.com/Temple%20Smith.jpg Image credit (Michael Waterman): http://www.iscb.org/cms_addon/conferences/ismb2003/images/watterman.jpg
- #5: Made alignment of human.fa and fly.fa using Needleman-wunsch with default parameters at: http://emboss.bioinformatics.nl/cgi-bin/emboss/needle (EMBOSS needle) Human Eyeless (PAX6) from: http://www.treefam.org/cgi-bin/TFseq.pl?id=ENST00000379111.1 D. Melanogaster Eyeless from: http://www.treefam.org/cgi-bin/TFseq.pl?id=FBtr0100396.5 Viewed in jalview, and saved as humanfly_needlemanwunsch.png
- #7: Made alignment of human.fa and fly.fa using Smith-Waterman with default parameters at: http://emboss.bioinformatics.nl/cgi-bin/emboss/water (EMBOSS) Human Eyeless (PAX6) from: http://www.treefam.org/cgi-bin/TFseq.pl?id=ENST00000379111.1 D. Melanogaster Eyeless from: http://www.treefam.org/cgi-bin/TFseq.pl?id=FBtr0100396.5 Viewed in jalview, and saved as humanfly_smithwaterman.png
- #11: In R: >library("Biostrings") >seq1 <- "GGCTCAATCA" >seq2 <- "ACCTAAGG" >sigma <- nucleotideSubstitutionMatrix(match = 2, mismatch = -1, baseOnly = TRUE) >pairwiseAlignment(seq1, seq2, substitutionMatrix = sigma, gapOpening = 0, gapExtension = -2, scoreOnly = FALSE,type="local") dFixedSubject (1 of 1) pattern: [3] CTCAA subject: [3] CT-AA score: 6 Also: >source("C:/Documents and Settings/Avril Coughlan/My Documents/Rfunctions.R") >dnasmithwaterman(seq1,seq2,gapopen=0,gapextend=-2,mymatch=2,mymismatch=-1) [1] "maxT= 6" NA G G C T C A A T C A NA NA NA NA NA NA NA NA NA NA NA NA A NA "0 +" "0 +" "0 +" "0 +" "0 +" "2 >" "2 >" "0 -" "0 +" "2 >" C NA "0 +" "0 +" "2 >" "0 -" "2 >" "0 L" "1 >" "1 >" "2 >" "0 L" C NA "0 +" "0 +" "2 >" "1 >" "2 >" "1 >" "0 +" "0 >" "3 >" "1 Z" T NA "0 +" "0 +" "0 |" "4 >" "2 -" "1 >" "0 >" "2 >" "1 |" "2 >" A NA "0 +" "0 +" "0 +" "2 |" "3 >" "4 >" "3 >" "1 -" "1 >" "3 >" A NA "0 +" "0 +" "0 +" "0 |" "1 V" "5 >" "6 >" "4 -" "2 -" "3 >" G NA "2 >" "2 >" "0 -" "0 +" "0 +" "3 |" "4 V" "5 >" "3 Z" "1 *" G NA "2 >" "4 >" "2 -" "0 -" "0 +" "1 |" "2 V" "3 V" "4 >" "2 Z“ NOTE: there seems to be a mistake in the Deonier book for this example on page 157 of Deonier – it has “... 2 3 4 3 2 1 3” on one row, but should have “ ... 2 3 4 3 1 1 3” on that row (row i =5).
- #15: In R: >library("Biostrings") >seq1 <- " TCAGTTGCC " >seq2 <- " AGGTTG " >sigma <- nucleotideSubstitutionMatrix(match = 1, mismatch = -2, baseOnly = TRUE) >pairwiseAlignment(seq1, seq2, substitutionMatrix = sigma, gapOpening = 0, gapExtension = -2, scoreOnly = FALSE,type="local") Local PairwiseAlignedFixedSubject (1 of 1) pattern: [4] GTTG subject: [3] GTTG score: 4 Also: >source("C:/Documents and Settings/Avril Coughlan/My Documents/Rfunctions.R") >dnasmithwaterman(seq1,seq2,gapopen=0,gapextend=-2,mymatch=1,mymismatch=-2) [1] "maxT= 4" NA T C A G T T G C C NA NA NA NA NA NA NA NA NA NA NA A NA "0 +" "0 +" "1 >" "0 +" "0 +" "0 +" "0 +" "0 +" "0 +" G NA "0 +" "0 +" "0 +" "2 >" "0 -" "0 +" "1 >" "0 +" "0 +" G NA "0 +" "0 +" "0 +" "1 >" "0 >" "0 +" "1 >" "0 +" "0 +" T NA "1 >" "0 +" "0 +" "0 +" "2 >" "1 >" "0 +" "0 +" "0 +" T NA "1 >" "0 +" "0 +" "0 +" "1 >" "3 >" "1 -" "0 +" "0 +" G NA "0 +" "0 +" "0 +" "1 >" "0 +" "1 |" "4 >" "2 -" "0 -"