<html><head></head><body><div class="ydpbf3e471eyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:10px;"><div></div>
<div dir="ltr" data-setdir="false">Can you show your code?</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Thanks,</div><div dir="ltr" data-setdir="false"><br></div><div><br></div>
</div><div id="yahoo_quoted_0258604357" class="yahoo_quoted">
<div style="font-family:'Helvetica Neue', Helvetica, Arial, sans-serif;font-size:13px;color:#26282a;">
<div>
On Wednesday, March 22, 2023 at 06:41:56 AM GMT+9, Vitoria Zanon <zanon.vih@gmail.com> wrote:
</div>
<div><br></div>
<div><br></div>
<div><div id="yiv7426750336"><div dir="ltr">Hello! I hope this email finds you well.<div><br></div><div>My name is Vitoria and I'm currently using Biopython to develop a new multiple sequence alignment tool as my PhD project, specially the Bio.pairwise2 method, which is the main reason I'm writing this email: the deprecated warning told me I should talk to you about this.</div><div><br></div><div>In my code, the pairwise2 method helps produce an alignment library which contains <i>(n²-n)/2</i> pairwise alignments, being <i>n</i> the number of sequences in the input file. This library helps the <a rel="nofollow noopener noreferrer" target="_blank" href="https://doi.org/10.1093/bioinformatics/14.5.407">COFFEE objective function</a> (NOTREDAME et al., 1998) to evaluate the MSAs produced by the tool. I was using the Bio.Align.PairwiseAlignment method but I faced an issue with it: I couldn't get the aligned sequences from the PairwiseAlignment object as a Seq object, String or neither a SeqRecord object. The library should keep the name of the sequences, the sequences itself and the alignment score, but all I was able to do is to get the target/query sequences (unaligned) or the Align object itself, which wouldn't work for me. However with pairwise2 i was able to get the sequences and work with them as i planned to. I must admit the PairwiseAlignment has a more intuitive and useful class structure and I already thought about using it in other projects from our lab, but it doesn't work for this specific project in specific. I'm also sending a print from my code to illustrate the pairwise2 use.</div><div><br></div><div>Therefore, I would like you to consider adding this feature in PairwiseAlignment or as a different method since you discontinued pairwise2. By now, my main objective is to finish the whole tool and test its results so I can get data about the performance of the new algorithm I'm proposing. After that I plan to make the tool available on the internet and I want to work with the latest releases from each library involved so it can work fine in any machine and improve its execution when the libraries themselves get improved.</div><div><br></div><div>Thank you for reading!</div><div><br></div><div>Sincerely yours, </div><div>Vitoria</div></div>
</div>_______________________________________________<br>Biopython mailing list - <a ymailto="mailto:Biopython@biopython.org" href="mailto:Biopython@biopython.org">Biopython@biopython.org</a><br><a href="https://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank">https://mailman.open-bio.org/mailman/listinfo/biopython</a><br></div>
</div>
</div></body></html>