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<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">Hi all,<o:p></o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">I am new to this mailing list. First of all many thanks for your work, I have happily used Biopython in several projects before.<o:p></o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">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: </span><span style="font-family:"Calibri",sans-serif;color:black"><a href="https://biopython.org/docs/1.76/api/Bio.codonalign.codonseq.html#Bio.codonalign.codonseq.cal_dn_ds" id="LPlnk889923"><span lang="EN-US">https://biopython.org/docs/1.76/api/Bio.codonalign.codonseq.html#Bio.codonalign.codonseq.cal_dn_ds</span></a></span><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">,
but this does not cover my needs. <o:p></o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">What I need is to compute dN/dS based on the count of mutations over a set of samples as explained at
</span><span style="font-family:"Calibri",sans-serif;color:black"><a href="https://bioinformatics.cvr.ac.uk/calculating-dnds-for-ngs-datasets/" id="LPlnk772882"><span lang="EN-US">https://bioinformatics.cvr.ac.uk/calculating-dnds-for-ngs-datasets/</span></a></span><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><img border="0" width="713" height="563" style="width:7.427in;height:5.8645in" id="img795255" src="cid:7c03806e-bbb0-47b1-9c49-3c53e33af83e" alt="cid:7c03806e-bbb0-47b1-9c49-3c53e33af83e"></span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">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.
<o:p></o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">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?<o:p></o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">Best wishes,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Segoe UI",sans-serif;color:#AD351F">Pablo Riesgo Ferreiro<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Segoe UI",sans-serif;color:#103D72">Computational Medicine</span><span style="font-size:10.0pt;font-family:"Segoe UI",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Segoe UI",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Segoe UI",sans-serif;color:#1F497D">
<b>TRON</b></span><span style="font-size:10.0pt;font-family:"Segoe UI",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Segoe UI",sans-serif;color:#1F497D">Translationale Onkologie an der Universitätsmedizin der</span><span style="font-size:10.0pt;font-family:"Segoe UI",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Segoe UI",sans-serif;color:#1F497D">Johannes Gutenberg-Universität Mainz gemeinnützige GmbH
</span><span style="font-size:10.0pt;font-family:"Segoe UI",sans-serif;color:#1F497D"><o:p></o:p></span></p>
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