[Bioperl-l] IUPAC code similarity

shalabh sharma shalabh.sharma7 at gmail.com
Fri Sep 17 11:07:38 EDT 2010


Thanks Aaron for your reply.
Actually i tried that first, but there is another problem, i have to divide
each query sequence to window size 5 with 1 base shift and its not possible
to divide regular expression in that way.
So what i am trying is to convert those iupac codes to 4 base code sequence
and then do the normal search.
Now the problem is that i cant able to convert those IUPAC sequences to
normal ones, i am still trying to write a script but its taking time.

Thanks
Shalabh


On Fri, Sep 17, 2010 at 10:28 AM, Aaron Mackey <amackey at virginia.edu> wrote:

> 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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>>
>
>


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