[Bioperl-l] IUB/IUPAC nucleic acid codes

[Richard Rouse]

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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