[Biopython] Calculating NS and S over a given sequence

[Riesgo Ferreiro, Pablo]

Thanks Zheng, I will look into the details of the implementation.


What I am in need is something like cal_n_s(ref_deq).  I will check if it makes any sense to make this a public function.



Best,

Pablo

________________________________
From: Zheng Ruan <zruan1991 at gmail.com>
Sent: 30 September 2021 15:32:38
To: Riesgo Ferreiro, Pablo
Cc: biopython at biopython.org
Subject: Re: [Biopython] Calculating NS and S over a given sequence

Hi Pablo,

You can simply use cal_dn_ds(ref_seq, sample_seq) to achieve this. If you have multiple sample_seqs, you may iterate all of them.

Internally, cal_dn_ds determines the N and S sites by averaging the N and S sites counted from both the ref_seq and sample seq. If you specify the NG86 method, it does the log transform as you show in the figure.

Best,
Zheng

On Thu, Sep 30, 2021 at 5:24 AM Riesgo Ferreiro, Pablo <Pablo.RiesgoFerreiro at tron-mainz.de<mailto:Pablo.RiesgoFerreiro at tron-mainz.de>> wrote:

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 Universitätsmedizin der
Johannes Gutenberg-Universität Mainz gemeinnützige GmbH

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