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Dear John,<br>
<br>
I did the rewrite of pairwise2 in 2016. Michiel, who wrote the new
PairwiseAligner, did some comparisons and, as far as I remember,
pairwise2 was comparable to the new PairwiseAligner regarding
maximum sequence length. Also, in my experience, ~2000 residues for
pairwise2 is very low; I usually got something about ~7000 residues.
Can you report a test case, e.g. two sequence IDs and your pairwise2
alignment parameters?<br>
<br>
Best,<br>
Markus<br>
<br>
<div class="moz-cite-prefix">Am 10.07.2018 um 20:51 schrieb John
Berrisford:<br>
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<p class="MsoNormal">Hi <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m looking at performing pairwise
alignments of polymer sequences in biopython. <o:p></o:p></p>
<p class="MsoNormal">These will be protein or nucleotide
sequences. They may include non-standard residues which will
be denoted as X. <o:p></o:p></p>
<p class="MsoNormal">The sequences will be of varying length
from around 20 residues up to several thousand residues – put
simply the range of sequences in the PDB. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m looking for the best tool to use to do
this in biopython<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">So far I have performed tests with
pairwise2 and Align.PairwiseAligner. <o:p></o:p></p>
<p class="MsoNormal">From my tests it seems that pairwise2 has a
limit of ~2000 residues – i.e. if I give it a sequence of 2500
residues to compare against itself it crashes. PairwiseAligner
seems to be able to handle much longer sequences without
issue. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I need to be able to set gap penalties –
which is possible in both of these programs. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">So my question are:<o:p></o:p></p>
<p class="MsoNormal">Are these the only options in biopython? –
I would prefer a python implementation rather than something
that requires external compilation i.e. Emboss Needle<o:p></o:p></p>
<p class="MsoNormal">Are these the best options?<o:p></o:p></p>
<p class="MsoNormal">Are they both maintained / stable? <o:p></o:p></p>
<p class="MsoNormal">Are they comparable in their results?<o:p></o:p></p>
<p class="MsoNormal">Is the limitation in sequence length in
pairwise2 a known issue? A quick google search suggests most
people use pairwise2, which is strange given its sequence
length limitation. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">John <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">--<o:p></o:p></p>
<p class="MsoNormal">John Berrisford<o:p></o:p></p>
<p class="MsoNormal">PDBe<o:p></o:p></p>
<p class="MsoNormal">European Bioinformatics Institute
(EMBL-EBI)<o:p></o:p></p>
<p class="MsoNormal">European Molecular Biology Laboratory<o:p></o:p></p>
<p class="MsoNormal">Wellcome Genome Campus<o:p></o:p></p>
<p class="MsoNormal">Hinxton<o:p></o:p></p>
<p class="MsoNormal">Cambridge CB10 1SD UK<o:p></o:p></p>
<p class="MsoNormal">Tel: +44 1223 492529<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><a href="https://www.pdbe.org/"
moz-do-not-send="true"><span style="color:#0563C1">https://www.pdbe.org</span></a><o:p></o:p></p>
<p class="MsoNormal"><a
href="https://www.facebook.com/proteindatabank"
moz-do-not-send="true"><span style="color:#0563C1">https://www.facebook.com/proteindatabank</span></a><o:p></o:p></p>
<p class="MsoNormal"><a href="https://twitter.com/PDBeurope"
moz-do-not-send="true"><span style="color:#0563C1">https://twitter.com/PDBeurope</span></a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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