[Bioperl-l] IUPAC code similarity
roy.chaudhuri at gmail.com
Fri Sep 17 11:04:28 EDT 2010
The expand method in Bio::Tools::SeqPattern may be useful to convert
IUPAC codes to regular expressions:
$perl -e 'use Bio::Tools::SeqPattern; print
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.
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.
> 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
>> 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.
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>> Bioperl-l at lists.open-bio.org
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