Carnë Draug | 4 Mar 02:58 2013
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Re: module for description of sequence variants (where to place code)

On 25 February 2013 10:32, Andreas Leimbach
<andreas.leimbach <at> uni-wuerzburg.de> wrote:
> On 25.2.13 11:08, Carnė Draug wrote:
>>
>> I'm writing a perl module to write a description of the variance
>> between 2 sequences as described on
>> http://www.hgvs.org/mutnomen/recs-prot.html
>>
>> Basically, given 2 sequences, would returns something like "p.Lys2del
>> p.His25_Met26insGln" if those are the differences. It also accounts
>> for the existence of - characters on the sequences that may come from
>> their alignment.
>>
>> My question is, where on the project tree should I place the module?
>>
>> Also, is there something already written that would convert from 1 to
>> 3 letter code?
>>
> for your last question:
> You can convert aa strings from one to three letter code with
> 'Bio::SeqUtils'.

Thank you. I have never used Bio::SeqUtils. Not only does solve my
problem, but also seems to be the right place to insert my code.

If no one objects, I'll add a new method to Bio::SeqUtils named
"describe_mutation".

Carnë

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