This represents the best possible alignment score

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Unformatted text preview: quot;). This represents the best possible alignment score. possible Extensions to basic dynamic programming alignment method s use similarity function in initialization step Similarity Functions s Used to facilitate comparison of two Used sequence elements sequence s logical valued (true or false, 1 or 0) x test whether first argument matches (or could test whether match) second argument match) s numerical valued x test degree to which first argument matches test degree second second Logical valued similarity functions s Let Search(I)=‘A’ and Sequence(J)=‘R’ Let Sequence(J)=‘R’ s A Function to Test for Exact Match x s MatchExact(Search(I),Sequence(J)) would return MatchExact(Search(I),Sequence(J)) FALSE since A is not R FALSE A Function to Test for Possibility of a Function Match using IUB codes for Incompletely Specified Bases Specified x MatchWild(Search(I),Sequence(J)) would return MatchWild(Search(I),Sequence(J)) TRUE since R can be either A or G TRUE Numerical valued similarity functions s return value could be probability (for DNA) x x s return value could be similarity (for protein) x x s Let Search(I) = 'A' and Sequence(J) = 'R' Let Sequence(J) SimilarNuc (Search(I),Sequence(J)) could return 0.5 SimilarNuc could 3 since chances are 1 out of 2 that a purine is adenine Let Seq1(I) = 'K' (lysine) and Seq2(J) = 'R' (arginine) Let (arginine) SimilarProt(Seq1(I),Seq2(J)) could return 0.8 SimilarProt(Seq1(I),Seq2(J)) could 3 since lysine is similar to arginine usually use integer values for efficiency Scoring (similarity) matrices s For each pair of characters in alphabet, For value is proportional to degree of similarity (or other scoring criterion) between them (or s For proteins, most frequently used is For Mutation Data Matrix from Dayhoff, 1978 (MDM78) (MDM Dayhoff PAM2...
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