Algorithms on Sequences

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Taylor’s Venn Diagram For usual protein properties Validation of an alignment • A computer program finds always a solution… • What is the credit that may be assigned to resulting alignments ? – Validation from : • the score ? • the percentage of identities ? • … • Problem : How to decide that an alignment has something to do with biological reality
Example 1 : easy case ALIGN calculates a global alignment of two sequences version 2.0uPlease cite: Myers and Miller, CABIOS (1989) 4:11-17 AF248645_1 150 aa vs. AF156936_1 149 aa scoring matrix: BLOSUM50, gap penalties: -12/-2 44.1% identity; Global alignment score: 428 10 20 30 40 50 60 /tmp/t MPIVDTGSVAPLSAAEKTKIRSAWAPVYSNYETSGVDILVKFFTSTPAAQEFFPKFKGLT :::.: : . :: ..: :: .: .:.:.: .:. .:..:. ..:.::. ::::.. AF1569 MPITDQGPLPTLSEGDKKAIRESWPQIYQNFEQTGLVVLLEFLQKNPGAQQSFPKFSA-- 10 20 30 40 50 70 80 90 100 110 120 /tmp/t TADQLKKSADVRWHAERIINAVNDAVVSMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVL : .:... .:.:.: ::::::: .. :: :.. :..::.::.. :::::. :: : AF1569 TKCNLEQDNEVKWQASRIINAVNHTIGLMDKEAAMKQYLKELSAKHSSEFQVDPKLFKEL 60 70 80 90 100 110 130 140 150 /tmp/t AAVIADTVAAGDAGFEKLMSMICILLRSAY-- .:....:. : :..:::.:.:: ::::.: AF1569 SAIFVSTIR-GKAAYEKLFSIICTLLRSSYDE 120 130 140 Example 2 : opposite but easy… ALIGN calculates a global alignment of two sequences version 2.0uPlease cite: Myers and Miller, CABIOS (1989) 4:11-17 U13831_1 134 aa vs. AF248645_1 150 aa scoring matrix: BLOSUM50, gap penalties: -12/-2 15.8% identity; Global alignment score: -47 10 20 30 40 50 /tmp/t MTRDQNGTWEMESNENFEGYMKALDIDFATPKIAVRLTQTKVI---DQDGDNFKTK---T : ..:. : :. : .: . . : . .: .. .: . AF2486 MPIVDTGSVAPLS---------------AAEKTKIRSAWAPVYSNYETSGVDILVKFFTS 10 20 30 40 60 70 80 90 100 110 /tmp/t TSTFRNYDVDFTVGVEFDEYTKSLDNR-HVKALVTWEGDVLVCVQKGEKENRGWKQW--- : . ... : . :. :: : : :.. ... .:..: .. :: . .. AF2486 TPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVVSMDDTEKMSMKLRDLSGK 50 60 70 80 90 100 120 130 /tmp/t ----IEGDKLYLEL---------TCGD--------QVCRQVFKKK .. : :... . :: ..: . . AF2486 HAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY 110 120 130 140 150
Page 1 and 2: Bioinformatics Algorithms</
Page 3 and 4: Alignment of two sequences • Matc
Page 5 and 6: DP applied to alignments • Given
Page 7 and 8: Needleman & Wunsh’s algorithm (4)
Page 9 and 10: Smith & Waterman algorithm (1) •
Page 11 and 12: E I,J = MAX Gotoh’s algorithm (2)
Page 13 and 14: Identity and default Blast Matrices
Page 15: Other substitution matrices • Phy
Page 19 and 20: Validation of a global alignment (2
Page 21 and 22: PRSS compares a test sequence to a
Page 23 and 24: BLASTN 1.4.7 [16-Oct-94] [Build 17:
Page 25 and 26: Principle of the heuristics (1) 1 -
Page 27 and 28: Tradeoff sensitivity / rapidity W 1
Page 29 and 30: Recent Blasts • Blast2 (Gapped Bl

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