[Bioperl-l] IUPAC code similarity

shalabh sharma shalabh.sharma7 at gmail.com
Fri Sep 17 16:45:50 EDT 2010


Thanks Aaron,
changing the query sequence worked well but i am still struggling with the
database.

-Shalabh


On Fri, Sep 17, 2010 at 3:25 PM, Aaron Mackey <amackey at virginia.edu> wrote:

> 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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