| 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. Types: LocalAlignmentFinder
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. See Also localAlignment, LocalAlignmentFinder, smithWatermanGetNext SeqAn - Sequence Analysis Library - www.seqan.de