[Bioperl-l] IUB/IUPAC nucleic acid codes

[Aaron J. Mackey]

Bio::Tools::IUPAC already does all this.

-Aaron

On Mar 26, 2004, at 3:17 PM, Richard Rouse wrote:

> Allen,
>
> So perhaps the input can be a fasta formatted file containing these 
> types of
> bases and the output will also be fasta formatted having all the
> combinations:
>
> INPUT
>> accession1
> VVCCAGGAWC
>> accession2
> TGGCACRCWT
>> accession3
> TNGSNYTNWTV
> _____________________________
>
> OUTPUT
> accession1
>> 1
> sequence
>> 2
> sequence
> 	etc .....
> accession2
>> 1
> sequence
>> 2
> sequence
> 	etc .....
>
> Richard
>
>
> -----Original Message-----
> From: Allen Day [mailto:allenday at ucla.edu]
> Sent: Friday, March 26, 2004 11:25 AM
> To: Richard Rouse
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] IUB/IUPAC nucleic acid codes
>
>
> no, i was looking for this recently too.  in my own dev libs i've 
> already
> written the code that can go from concrete (ie, ATCG) sequence to
> degenerate if you supply the degenerate letters you want to allow.  i 
> have
> some code that does what you ask too.  i'll commit it into bioperl when
> it's a little more mature.
>
> can you give your use case, possibly with an example of how you'd like 
> to
> use the api?
>
> -allen
>
>
>
> On Fri, 26 Mar 2004, Richard Rouse wrote:
>
>>
>>
>> Does anyone know if bioperl has a tool that can generate all the 
>> possible
>> sequence combinations from a sequence like this:
>>
>> VMARAYTYKHKRAAAASABKTCCA
>>
>>
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>
>
>
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