Refine Shake

Calling Sequences:
Refine Shake(m, DM)
Parameters:

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