[Biopython] Biopython Digest, Vol 224, Issue 6

[Daniel Gonzalez-Ibeas]

Hi Pablo,

For this analysis PAML is a gold standard. You can give a glimpse here:

https://biopython.org/wiki/PAML

in case it covers your needs.

Best regards,

Daniel.





> ----------------------------------------
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> Sent: Thu Sep 30 11:24:37 CEST 2021
> To: <biopython at biopython.org>
> Subject: Biopython Digest, Vol 224, Issue 6
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> Today's Topics:
> 
>    1. Calculating NS and S over a given sequence
>       (Riesgo Ferreiro, Pablo)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 30 Sep 2021 08:07:53 +0000
> From: "Riesgo Ferreiro, Pablo" <Pablo.RiesgoFerreiro at TrOn-Mainz.DE>
> To: "biopython at biopython.org" <biopython at biopython.org>
> Subject: [Biopython] Calculating NS and S over a given sequence
> Message-ID: <95ae083a057843719a767b67feca0afe at TrOn-Mainz.DE>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi all,
> 
> 
> 
> 
> 
> I am new to this mailing list. First of all many thanks for your work, I have happily used Biopython in several projects before.
> 
> 
> 
> 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: https://biopython.org/docs/1.76/api/Bio.codonalign.codonseq.html#Bio.codonalign.codonseq.cal_dn_ds, but this does not cover my needs.
> 
> 
> 
> What I need is to compute dN/dS based on the count of mutations over a set of samples as explained at https://bioinformatics.cvr.ac.uk/calculating-dnds-for-ngs-datasets/
> 
> 
> 
> [cid:7c03806e-bbb0-47b1-9c49-3c53e33af83e]
> 
> 
> 
> 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.
> 
> 
> 
> 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?
> 
> 
> 
> 
> 
> 
> 
> Best wishes,
> 
> Pablo Riesgo Ferreiro
> Computational Medicine
> 
> ?TRON
> Translationale Onkologie an der Universit?tsmedizin der
> Johannes Gutenberg-Universit?t Mainz gemeinn?tzige GmbH?
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