[Bioperl-l] IUPAC code similarity

Aaron Mackey amackey at virginia.edu
Fri Sep 17 15:25:54 EDT 2010


do your windowing/shifting on the unexpanded query sequences; then transform
the 5-bp queries into regular expressions.

-Aaron

On Fri, Sep 17, 2010 at 11:07 AM, shalabh sharma
<shalabh.sharma7 at gmail.com>wrote:

> 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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>


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