m | : | Match |
DM | : | DayMatrix |
Returns: Match
Synposis: The LocalAlign function implements the Smith-Waterman algorithm [25] to find the best local alignment, ie. an alignment which is a subsequence of the amino acid sequences m1 and m2 contained in m. It computes this alignment at PAM distance defined by the similarity matrix DM.
Examples:
> DB := ReadDb('~cbrg/DB/SwissProt'): CreateDayMatrices(): > m := Match(op(Sequence(Entry(8588))), op(Sequence(Entry(8577)))): > m := LocalAlign(m, DM); # compute best local alignment at 250 PAM > print(m);
FindEntropy EstimatePam FindLongestRep PItoPAM PAMtoPI ProbDynProg DynProgStrings WriteFasta WriteMsa WriteMSADB