[Biopython] Biopython Digest, Vol 224, Issue 7

Fri Oct 1 13:46:53 EDT 2021

Thanks Daniel.

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.

Best wishes,
Pablo
________________________________
From: Biopython <biopython-bounces at biopython.org> on behalf of biopython-request at biopython.org <biopython-request at biopython.org>
Sent: 30 September 2021 18:00:02
To: biopython at biopython.org
Subject: Biopython Digest, Vol 224, Issue 7

Send Biopython mailing list submissions to
        biopython at biopython.org

To subscribe or unsubscribe via the World Wide Web, visit
        https://mailman.open-bio.org/mailman/listinfo/biopython
or, via email, send a message with subject or body 'help' to
        biopython-request at biopython.org

You can reach the person managing the list at
        biopython-owner at biopython.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Biopython digest..."

Today's Topics:

   1. Re: Biopython Digest, Vol 224, Issue 6 (Daniel Gonzalez-Ibeas)

----------------------------------------------------------------------

Message: 1
Date: Thu, 30 Sep 2021 13:12:24 +0200 (CEST)
From: Daniel Gonzalez-Ibeas <danielglz at mailfence.com>
To: biopython at biopython.org
Subject: Re: [Biopython] Biopython Digest, Vol 224, Issue 6
Message-ID: <43727389.578320.1633000344877 at ichabod.co-bxl>
Content-Type: text/plain; charset=utf-8

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.

> ----------------------------------------
> From: <biopython-request at biopython.org>
> Sent: Thu Sep 30 11:24:37 CEST 2021
> To: <biopython at biopython.org>
> Subject: Biopython Digest, Vol 224, Issue 6
>
>
> Send Biopython mailing list submissions to
>        biopython at biopython.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        https://mailman.open-bio.org/mailman/listinfo/biopython
> or, via email, send a message with subject or body 'help' to
>        biopython-request at biopython.org
>
> You can reach the person managing the list at
>        biopython-owner at biopython.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biopython digest..."
>
>
> 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?
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20210930/96484e77/attachment.htm>
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: Screenshot from 2021-09-30 09-55-58.png
> Type: image/png
> Size: 100309 bytes
> Desc: Screenshot from 2021-09-30 09-55-58.png
> URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20210930/96484e77/attachment.png>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Biopython mailing list  -  Biopython at biopython.org
> https://mailman.open-bio.org/mailman/listinfo/biopython
>
>
> ------------------------------
>
> End of Biopython Digest, Vol 224, Issue 6
> *****************************************

--?
Sent with https://mailfence.com
Secure and private email

--
Sent with https://mailfence.com
Secure and private email

------------------------------

Subject: Digest Footer

_______________________________________________
Biopython mailing list  -  Biopython at biopython.org
https://mailman.open-bio.org/mailman/listinfo/biopython

------------------------------

End of Biopython Digest, Vol 224, Issue 7
*****************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20211001/607e3159/attachment.htm>