[Bioperl-l] IUPAC code similarity

Aaron Mackey amackey at virginia.edu
Fri Sep 17 10:28:15 EDT 2010


Convert the IUPAC code to a regular expression, and use regular expressions
(in Perl or grep or similar) to find 100% identical matches.

-Aaron

On Thu, Sep 16, 2010 at 5:38 PM, shalabh sharma
<shalabh.sharma7 at gmail.com>wrote:

> Hi All,
>      I have few nucleotide sequences that are composed of IUPAC codes. Like
> >test
> VGSRVBSSSSSNSC
>
> Similarly i have a database made of of these kind of sequences. I want to
> find sequences that are 100% similar to the query sequence.
>
> Is there any bioPerl module to deal with this, i tried normal blast but it
> didn't worked.
> Do i have to convert these sequences to 4 base codes or there is any other
> way out.
>
> Thanks
> Shalabh
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