smithWatermanGetNext

Function

Computes next best local alignment.

Declumps the matrix and computes the next best local alignment of the (two) sequences given in align according to the score values given in score. Declumping means forbidding all matches and mismatches that were used in previously found alignment to be used again.

smithWatermanGetNext(align, sw_finder, score, cutoff)

Parameters

align	The alignment object having the sequences to be aligned as sources. Types: Align
sw_finder	The local alignment finder object (that has been passed to smithWaterman before). Types: LocalAlignmentFinder
score	The score values to be used for computing the alignment. Types: Score
cutoff	Alignments with scores < cutoff will be discarded. Remarks: Only use a cut off score that is greater or equal to the one that was used when calling smithWaterman.

Return Values

The score value of the next best local alignment or 0 if there was no alignment with score > cutoff.

The corresponding alignment can be found in align.