[Bioperl-l] IUPAC code similarity

Aaron Mackey amackey at virginia.edu
Fri Sep 17 15:24:44 EDT 2010


If there are ambi. codes in the database, then the expanded character class
has to also include the original ambiguity code; non-ambiguous nucleotides
must also be expanded to include all ambiguity codes that represent the
nucleotide.

-Aaron

On Fri, Sep 17, 2010 at 11:04 AM, Roy Chaudhuri <roy.chaudhuri at gmail.com>wrote:

> Hi Shalabh,
>
> The expand method in Bio::Tools::SeqPattern may be useful to convert IUPAC
> codes to regular expressions:
>
> $perl -e 'use Bio::Tools::SeqPattern; print
> Bio::Tools::SeqPattern->new(-seq=>"VGSRVBSSSSSNSC", -type=>'DNA')->expand'
> [ACG]G[GC][AG][ACG][CGT][GC][GC][GC][GC][GC].[GC]C
>
> Although that won't work if there are also abiguity codes in your database.
> For a non-BioPerl solution you could try fuzznuc from Emboss.
>
> Cheers.
> Roy.
>
>
> On 17/09/2010 15:28, Aaron Mackey 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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