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Introduction Sequence Alignment

, , Fall 2011 IntroductionSequence AlignmentMotivation: assess similarity of sequences and learn about theirevolutionary relationshipWhy do we want to know this?Example:SequencesACCCGAACTATCCTA alignAlignmentACCCGAAC--TATCC-TAHomology : Alignment reasonable, if sequences homologousACCGAACCCGAACCTATCCTATCTCACTAD efinition ( Sequence Homology)Two or more sequences arehomologousiffthey evolved from a common ancestor.[Homology in anatomy] , , Fall 2011 IntroductionPlan (and Some Preliminaries) First: study only pairwise , such that 6 . is called thegap elements of are twosequences a,b . For pairwise Sequence comparison: define edit distance, definealignment distance, show equivalence of distances, definealignment problem and efficient algorithmgap penalties, local Alignment Later: extend pairwise Alignment to multiple alignmentDefinition (Alphabet, words)Analphabet is a finite set (ofsymbols/characters).

For pairwise sequence comparison: de ne edit distance, de ne alignment distance, show equivalence of distances, de ne alignment problem and e cient algorithm gap penalties, local alignment Later: extend pairwise alignment to multiple alignment De nition (Alphabet, words) An alphabet is a nite set (of symbols/characters). + denotes

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