[Biopython-dev] [Bug 2776] New: Bio.pairwise2 returns non-optimal alignment in at least some cases

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2776

           Summary: Bio.pairwise2 returns non-optimal alignment in at least
                    some cases
           Product: Biopython
           Version: 1.49
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: klaus.kopec at tuebingen.mpg.de


At least in some cases, Bio.pairwise2 returns an alignment that is not the one
with the highest score for the input parameters. This occurs in localXX and
globalXX.

Yet, I only encountered the problem with large mismatch values (which I use as
I need mismatch free alignments).

simple example (the bug also occured for longer sequences):
>>> sequence1 = 'GKG'
>>> sequence2 = 'GWG'
>>> A = pairwise2.align.globalms(sequence1, sequence2, 5, -100, -5, -5)[0]
>>> A[0]
'GKG--'
>>> A[1]
'--GWG'
>>> A[2]
-15.0

whereas
'GK-G'
'G-WG'

would get a score of 0


System: Kubuntu 8.10 64Bit, Python 2.6.1, Biopython 1.49 (my pairwise2.py is
identical to the current CVS version of it)


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