[Biopython-dev] [Bug 2776] New: Bio.pairwise2 returns non-optimal alignment in at least some cases
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Mon Mar 2 15:22:53 UTC 2009
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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