Function
smithWaterman
Computes the best local alignment of the (two) sequences given in align.
smithWaterman(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.
score
The score values to be used for computing the alignment.
Types: Score
cutoff
A score limit.
Remarks: Alignments with scores < cutoff will be discarded (starTCGCGCCTGGAC CAAGACA ts being useful when not only the best, but also sub-optimal local aligments are of interest). Low cutoff scores cause a higher runtime.
Return Values
The score value of the best scoring local alignment or 0 if there was no alignment with score > cutoff.
align
The corresponding alignment.
Remarks
So far, only linear gap costs are allowed.
SeqAn - Sequence Analysis Library - www.seqan.de