slides-alignment-2

slides-alignment-2 - Computational Biology - p.1/26 String...

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Unformatted text preview: Computational Biology - p.1/26 String Alignment II Computational Biology, Department Informatik ETH Zentrum Computational Biology - p.2/26 Review of Last Week Mutation Matrices Dynamic programming Tabular computation - Matches, Mismatches, or Spaces (gaps, indels, deletions, insertions) Traceback Global Align Global Align Cost-free end gaps Local Align- -- Computational Biology - p.3/26 Organization Gaps Dyanmic programming - Formal definition - follows Gusfiled Algorithms on Strings, Trees and Sequences Chapter 11 Gap Placement- the unsolved problem Gap Penalties and dynamic programming constant arbitrary linear (Affine) convex Time analysis Linear space dynamic programming two----NISPLWFSDTRGNIPKLSVWLDDPQGSEPDMFNHFA G a p s Random sequence mutated 200 PAM units with deletions default - gap open penalty - 10.00, gap extension penalty .10 one TLTKEATQMIVLNNIGLGAETEENNEVLAQPGHDDCERTTETVMVCIAKLYDCSEY two TGAGHNLFMIFLDHHNGTVKEGEKYMNAVVTGSDHLVENSVVLMI---- LYRYGAY ** * * * * * ** * one YAMYWVSTLKFTNGLQDQITRKLIVKQPSTEVPSVLSYLS gap open penalty 1.0, gap extension penalty .05 one two one two TLTKEATQMIVLNN-IGLGAETEE-NNEVLAQPGHDDCERTTETVMVCIAKLYDCS TGAGHNLFMIFLDHHNGTVKEGEKYMNAVVT--GSDHLVENSVVLMI----LYRYG ** * * * * * * * * * ** . . .. .. . . SRYAMYWVSTLKFTNGLQDQITRKLIVKQPSTEVPSVLSYLS SNISPLWFSD---TRGNIPKLSVWLDDPQ-GSE-PDMFNHFA gap open penalty 0, gap extension penalty 0 one two one two TLTK EATQ MIVL NN- IGLG AETE E- NNEVLAQPGHDDCERTTETVMVCIAKLYDCS TGAGHNLFMIFLDHHNGTVKEGEKYMNAVVT--GSDHLVENSVVLMI----LYRYG ** * * * * * * * * * ** . . .. .. . . SRYAMYWVSTLKFTNGLQDQITRKLIVKQ--PS-TEVPSVLSY & 4 utational Biology – p.4/26 SNISPLWFSD---TRG---NIP-KLSVWLDDPQGSE-PDMFNHFA Computational Biology - p.5/26 Gap Weights A constant Gap Penalty implies that the cost of aligning---- a n d __-H---Y H Y are the same. A better model of gap placement says that it is easier to add a second space to an existing gap than to open a new gap. mechanisms of insertion- deletion events more likely to happen in loops slippage of DNA machinery It is more likely that 1 strand of 6 spaces is deleted than 6 strands of 1 space. A gap of more than one space can be created by one mutational event. A more plausible model treats the spaces in a gap not as separate events. Computational Biology - p.6/26 Review of Dynamic Programming 1) recurrence relation -establishes a recursive relationship between D(i,j) and values of D with index pairs smaller than i and j. When there are no smaller indices then the value of D(i,j) must be stated explicitly in the base conditions for D(i,j). 2) base conditions - Cost to transform the first i characters of one string into zero characters of the other string. Cost of deleting the first i characters....
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This note was uploaded on 02/13/2012 for the course CS 91.510 taught by Professor Staff during the Fall '09 term at UMass Lowell.

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slides-alignment-2 - Computational Biology - p.1/26 String...

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