[Biopython] Is there any Biopython tool to degenerate a nucleotide sequence

[Sampson, Jared]

Hi Jeremy -

Nice work, thanks for sharing.

However (and someone please correct me if I'm wrong here!), it looks like the current Leucine substitution, "YTN" would also match both of Phe's codons ("TTT" and "TTC"), and the current Arginine ("MGN") also matches two of Serine's codons ("AGT" and "AGC").  FWIW, the PhyloTools script<http://www.phylotools.com/ptdegenwebservice.htm> also produces the same erroneous degenerate codons.  I've sent the contact address on that site a bug report.

I've updated a fork<https://gist.github.com/jaredsampson/afe24bd0f002d818bb90> of your original gist to implement fixes for these residues, along with a couple stylistic changes (hope you don't mind).  Please feel free to incorporate them into your original.  If you want to double check the rest of the degen_dict, there's a nice table on Wikipedia<https://en.wikipedia.org/wiki/Codon_degeneracy#Terminology>.

Also, if you're looking to make other improvements, it might be nice to add a "frame=1" argument to degenerate_sequence() to optionally accommodate the other two reading frames rather than chopping leftover bases.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jul 31, 2015, at 1:39 AM, Jeremy <Jeremy.molbio at gmail.com<mailto:Jeremy.molbio at gmail.com>> wrote:

Carlos Pena <mycalesis <at> gmail.com<http://gmail.com/>> writes:


Dear Biopython members,

I want to take a nucleotide string and degenerate those bases that can
undergo synonymous change.

For example, a string of just one codon.

* Input:  AAC
* Output:  AAY

Since both AAC and AAT are translated to Asparagine (N) we can
degenerate this codon to AAY (because the third position could produce a
synonymous change).

This is already solved in the Perl library Degen
http://www.phylotools.com/ptdegendocumentation.htm

I could use some glue to execute this Perl code from Python but
I cannot include this library in my project because they are using the
GPL license while I use BSD.

So I thought asking around before writing a Python script to do this for
me.

thanks for any pointers,

carlos



Hi Carlos,

I hacked up something that should return the same output as the Degen 1.4
Perlweb tool.

The gist can be found here:

https://gist.github.com/biojerm/6242381eb4ad3ef18ac6

I am pretty new to both Python and Biopython, so the please let me know if
you have any feedback on both form, styling, and/or function.

I know the method is currently quite fragile. Below are a few thoughts on
the method's weaknesses

1)The method does not handle sequences that are not evenly divisible by 3.

2)I think the method would be a lot more useful if you could call it on a
single or set of FASTA files or a GB files.  But, I have not learned  how
to program that yet.

3) I probably should return the degenerate sequences as Seq files, but at
the moment they are simple strings.

4)Tests...need to figure those out too.


Please let me know if you find this useful or and if there are any must
have features for your purposes.

Thanks,
Jeremy



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