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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link="#0563C1" vlink="#954F72"><div class=WordSection1><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/"><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"><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"><span style='color:#0563C1'>https://twitter.com/PDBeurope</span></a><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>