User: sanner

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sanner20
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s*****@scripps.edu

Posts by sanner

<prev • 4 results • page 1 of 1 • next >
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Answer: A: Biopython pairwise sequence alignment behavior change between 1.59 and 1.76
... Markus Piotrowski gave a nice explanation and solution The aim of a pairwise alignment algorithm is to achieve an alignment with the best score (or the least costs). From the view of the algorithm (here Needleman-Wunsch-Gotoh) the situation "one gap in seqA followed by one gap in seqB" is not forbi ...
written 13 days ago by sanner20 • updated 13 days ago by genomax91k
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Comment: C: Biopython pairwise sequence alignment behavior change between 1.59 and 1.76
... I tried with 1.9 and get the same behavior so I did submit an issue to github. Thanks ...
written 13 days ago by sanner20
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Comment: A: Biopython pairwise sequence alignment behavior change between 1.59 and 1.76
... Thanks Joe I replaced ? by X which should stand for 'ANY' in the FASTA format but I get the same result. JC, My issue is that I expect pairwise2.align.globalxx('EPQYEEIPIYL', 'EPQXEEIPIYL') to return a 1 to one mapping with Y mapped to X as it use to do in 1.7 instead of creating a insertion in bot ...
written 21 days ago by sanner20
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Biopython pairwise sequence alignment behavior change between 1.59 and 1.76
... Hello I am in the process of porting code from Python 2.7 to 3.7 and I am running into some differences in BioPython The following 3 lines of code: from Bio import pairwise2 aln = pairwise2.align.globalxx('EPQYEEIPIYL', 'EPQ?EEIPIYL', one_alignment_only=True)[0] print(aln) on Python ...
software error alignment sequence written 23 days ago by sanner20

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