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<div>Thanks Daniel.<br>
<br>
My starting point are VCF files containing the mutations, not sequences. I could try to reconstruct the sequences by combining VCF and reference genome, but counting mutations is much simpler in my case. Probably not the best methodology, but I just want an
initial estimate.<br>
<br>
<br>
Best wishes,<br>
Pablo
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Biopython <biopython-bounces@biopython.org> on behalf of biopython-request@biopython.org <biopython-request@biopython.org><br>
<b>Sent:</b> 30 September 2021 18:00:02<br>
<b>To:</b> biopython@biopython.org<br>
<b>Subject:</b> Biopython Digest, Vol 224, Issue 7</font>
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Today's Topics:<br>
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1. Re: Biopython Digest, Vol 224, Issue 6 (Daniel Gonzalez-Ibeas)<br>
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----------------------------------------------------------------------<br>
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Message: 1<br>
Date: Thu, 30 Sep 2021 13:12:24 +0200 (CEST)<br>
From: Daniel Gonzalez-Ibeas <danielglz@mailfence.com><br>
To: biopython@biopython.org<br>
Subject: Re: [Biopython] Biopython Digest, Vol 224, Issue 6<br>
Message-ID: <43727389.578320.1633000344877@ichabod.co-bxl><br>
Content-Type: text/plain; charset=utf-8<br>
<br>
Hi Pablo,<br>
<br>
For this analysis PAML is a gold standard. You can give a glimpse here:<br>
<br>
<a href="https://biopython.org/wiki/PAML">https://biopython.org/wiki/PAML</a><br>
<br>
in case it covers your needs.<br>
<br>
Best regards,<br>
<br>
Daniel.<br>
<br>
<br>
<br>
<br>
<br>
> ----------------------------------------<br>
> From: <biopython-request@biopython.org><br>
> Sent: Thu Sep 30 11:24:37 CEST 2021<br>
> To: <biopython@biopython.org><br>
> Subject: Biopython Digest, Vol 224, Issue 6<br>
> <br>
> <br>
> Send Biopython mailing list submissions to<br>
> biopython@biopython.org<br>
> <br>
> To subscribe or unsubscribe via the World Wide Web, visit<br>
> <a href="https://mailman.open-bio.org/mailman/listinfo/biopython">https://mailman.open-bio.org/mailman/listinfo/biopython</a><br>
> or, via email, send a message with subject or body 'help' to<br>
> biopython-request@biopython.org<br>
> <br>
> You can reach the person managing the list at<br>
> biopython-owner@biopython.org<br>
> <br>
> When replying, please edit your Subject line so it is more specific<br>
> than "Re: Contents of Biopython digest..."<br>
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> <br>
> Today's Topics:<br>
> <br>
> 1. Calculating NS and S over a given sequence<br>
> (Riesgo Ferreiro, Pablo)<br>
> <br>
> <br>
> ----------------------------------------------------------------------<br>
> <br>
> Message: 1<br>
> Date: Thu, 30 Sep 2021 08:07:53 +0000<br>
> From: "Riesgo Ferreiro, Pablo" <Pablo.RiesgoFerreiro@TrOn-Mainz.DE><br>
> To: "biopython@biopython.org" <biopython@biopython.org><br>
> Subject: [Biopython] Calculating NS and S over a given sequence<br>
> Message-ID: <95ae083a057843719a767b67feca0afe@TrOn-Mainz.DE><br>
> Content-Type: text/plain; charset="utf-8"<br>
> <br>
> Hi all,<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> I am new to this mailing list. First of all many thanks for your work, I have happily used Biopython in several projects before.<br>
> <br>
> <br>
> <br>
> I have a need to compute the dN/dS ratio over a set of samples of the same species. I know this is not great 10.1371/journal.pgen.1000304, but still. I have found this feature in biopython calculating the dN/dS between sequences:
<a href="https://biopython.org/docs/1.76/api/Bio.codonalign.codonseq.html#Bio.codonalign.codonseq.cal_dn_ds">
https://biopython.org/docs/1.76/api/Bio.codonalign.codonseq.html#Bio.codonalign.codonseq.cal_dn_ds</a>, but this does not cover my needs.<br>
> <br>
> <br>
> <br>
> What I need is to compute dN/dS based on the count of mutations over a set of samples as explained at
<a href="https://bioinformatics.cvr.ac.uk/calculating-dnds-for-ngs-datasets/">https://bioinformatics.cvr.ac.uk/calculating-dnds-for-ngs-datasets/</a><br>
> <br>
> <br>
> <br>
> [cid:7c03806e-bbb0-47b1-9c49-3c53e33af83e]<br>
> <br>
> <br>
> <br>
> N and S is dependent on the reference sequence and independent on the samples. N and S can be calculated on different genomic regions (eg: coding region, transcript, exon, domain, etc.). The simplest input for this tool would be a given ORF sequence and you
would think of more complete things as a GFF file.<br>
> <br>
> <br>
> <br>
> It is a small thing, but unless anyone knows of an existing implementation, I think it may be useful to others. Do you think this would be a valuable contribution to biopython?<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> Best wishes,<br>
> <br>
> Pablo Riesgo Ferreiro<br>
> Computational Medicine<br>
> <br>
> ?TRON<br>
> Translationale Onkologie an der Universit?tsmedizin der<br>
> Johannes Gutenberg-Universit?t Mainz gemeinn?tzige GmbH?<br>
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