[Biopython] unusual genetic code

[Peter Cock]

On Tue, Sep 14, 2010 at 3:47 AM, Jessica Grant wrote:
>On Mon, Sep 13, 2010 at 9:49 PM, Peter Cock wrote:
>> On Mon, Sep 13, 2010 at 7:43 PM, Jessica Grant wrote:
>>>
>>> Hello,
>>>
>>> I am working with an organism that has an unusual genetic code.  Is there
>>> a way I can use biopython's translate() but import my own codon table
>>> instead of using the standard ncbi tables that are coded in the CodonTable
>>> module?
>>>
>>> Thanks!
>>>
>>> Jessica
>>
>> Hi Jessica,
>>
>> Good question - this is something I had thought about but not done anything
>> since no one had ever asked about using a non-standard table. After all, the
>> NCBI do have a pretty comprehensive list. I'm curious which organism(s) you
>> are using.
>>
>> In answer to your query, right now, not easily. However, it would be simple to
>> tweak the Bio.Seq module to allow the table argument to be a string or integer
>> as now (for referring to a built in NCBI table) or a CodonTable object which you
>> would have to supply. These are defined in the Bio.Data.CodonTable module.
>> If this sounds useful and you could help with testing, it could be done ready
>> for the next release of Biopython.
>>
>> Peter
>
> Thanks Peter,
>
> We are doing some work on a ciliate called Chilodonella uncinata.  It
> apparently has only one stop codon and the others are recoded in an
> unusual way so it doesn't quite fit any of the ncbi tables.
>
> I did try to play around with the CodonTable module, but couldnt' quite
> figure out how to do it.  Just making a new table similar to the tables that
> are in the module didn't do it, and I didn't feel comfortable messing around
> in the depths of biopython.  :)
>
> I would be happy to help with testing and I guess in the meantime I will be
> putting lots of if statements in my script.
>
> Jessica

Hi Jessica,

Do you have the information for the CodonTable handy? e.g. a list of the
start codons, and how to translate the 64 codons (including stop codons).
Given that I could show you how to make the CodonTable object.

Peter