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Unformatted text preview: String Alignment II Computational Biology, Department Informatik ETH Zentrum Computational Biology – p.1/26 R e v i e w o f L a s t W e e k Mutation Matrices Dynamic programming Tabular computation  Matches, Mismatches, or Spaces (gaps, indels, deletions, insertions) Traceback Global Align Global Align Costfree end gaps Local Align Computational Biology – p.2/26 O r g a n i z a t i o n 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 Computational Biology – p.3/26 G a p s Random sequence mutated 200 PAM units with deletions default  gap open penalty  10.00, gap extension penalty .10 one TLTKEATQMIVLNNIGLGAETEENNEVLAQPGHDDCERTTETVMVCIAKLYDCSE Y two TGAGHNLFMIFLDHHNGTVKEGEKYMNAVVTGSDHLVENSVVLMILYRYGA Y * . ** * . . * * * .. .*. ** * one YAMYWVSTLKFTNGLQDQITRKLIVKQPSTEVPSVLSYLS twoNISPLWFSDTRGNIPKLSVWLDDPQGSEPDMFNHFA gap open penalty 1.0, gap extension penalty .05 one TLTKEATQMIVLNNIGLGAETEENNEVLAQPGHDDCERTTETVMVCIAKLYDC S two TGAGHNLFMIFLDHHNGTVKEGEKYMNAVVTGSDHLVENSVVLMILYRY G * . ** * . * * * * *.. * * .. .*. ** one SRYAMYWVSTLKFTNGLQDQITRKLIVKQPSTEVPSVLSYLS two SNISPLWFSDTRGNIPKLSVWLDDPQGSEPDMFNHFA gap open penalty 0, gap extension penalty 0 one TLTKEATQMIVLNNIGLGAETEENNEVLAQPGHDDCERTTETVMVCIAKLYDC S two TGAGHNLFMIFLDHHNGTVKEGEKYMNAVVTGSDHLVENSVVLMILYRY G * . ** * . * * * * *.. * * .. .*. ** one SRYAMYWVSTLKFTNGLQDQITRKLIVKQPSTEVPSVLSYLS two SNISPLWFSDTRGNIPKLSVWLDDPQGSEPDMFNHFA Computational Biology – p.4/26 G a p W e i g h t s A constant Gap Penalty implies that the cost of aligning__ and__HYHY 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 insertiondeletion 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.5/26 R e v i e w o f D y n a m i c P r o g r a m m i n g 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.
 Fall '09
 Staff
 C Programming

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