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String Matching

String Matching. String matching: definition of the problem (text,pattern). depends on what we have: text or patterns. Exact matching:. The patterns ---> Data structures for the patterns. 1 pattern ---> The algorithm depends on |p| and | |.

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String Matching

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  1. String Matching String matching: definition of the problem (text,pattern) depends on what we have: text or patterns • Exact matching: • The patterns ---> Data structures for the patterns • 1 pattern ---> The algorithm depends on |p| and || • k patterns ---> The algorithm depends on k, |p| and || • Extensions • Regular Expressions • The text ----> Data structure for the text (suffix tree, ...) • Approximate matching: • Dynamic programming • Sequence alignment (pairwise and multiple) • Sequence assembly: hash algorithm • Probabilistic search: Hidden Markov Models

  2. Bioinformatics Pairwise and multiple alignment

  3. Pairwise alignment + - s(A,CTAC)-2 s(AC,CTACT)=maximum s(A,CTA) 1 s(AC,CTA)-2 Edit distance: match=0 mismatch=1 indel=1 d(A,CTAC)+1 d(AC,CTACT)=minimum d(A,CTA)….+1 d(AC,CTA)+1 Similarity: match=1 mismatch=-1 indel=-2

  4. Pairwise alignment Connect to http://alggen.lsi.upc.es Links to TEACHING EMBER LePA

  5. Multiple alignment alignment

  6. Pairwise to multiple alignment S2 A C A -1 S3 __ S1 What happens with three strings? Let n be their lenght, then the cost becomes O(n3) “O(23)” “O(32)” And with k strings? O(nk 2k k2)

  7. Multiple alignment Programs of multialignment use different heuristics: • Clustal (Progressive alignment) http://www.ebi.ac.uk/clustalw • TCoffee (Progressive alignment + data bases) http://igs-server.cnrs-mrs.fr/Tcoffee_cgi/index.cgi • HMM (Hidden Markov Models)

  8. Multiple alignment Connect to http://alggen.lsi.upc.es/ and follow the links TEACHING EMBER.

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