Function
smithWaterman
Computes the best local alignment of the (two) sequences given in align.
Parameters
The alignment object having the sequences to be aligned as sources. Types: Align | |
The local alignment finder object. Types: LocalAlignmentFinder | |
The score values to be used for computing the alignment. Types: Score | |
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.
The corresponding alignment. |
Remarks
So far, only linear gap costs are allowed.
SeqAn - Sequence Analysis Library - www.seqan.de