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localms(sequenceA, sequenceB, match, mismatch, open, extend) -> alignments

match is the score to given to identical characters.  mismatch is
the score given to non-identical ones.

open and extend are the gap penalties when a gap is opened and
extended.  They should be negative.

alignments is a list of tuples (seqA, seqB, score, begin, end).
seqA and seqB are strings showing the alignment between the(more...)

src/b/c/bcbb-HEAD/align/adaptor_trim.py   bcbb(Download)
        adapt_region = adaptor
    else:
        aligns = pairwise2.align.localms(str(seq), str(adaptor),
                5.0, -4.0, -9.0, -0.5, one_alignment_only=True,
                gap_char=gap_char)

src/f/a/fastools-0.9.0/fastools/fastools.py   fastools(Download)
 
    for record in SeqIO.parse(inputHandle, "fasta"):
        alignment = pairwise2.align.localms(str(record.seq),
            tag, 1, -1, 0, -1)