[Bioperl-l] IUPAC code similarity

shalabh sharma shalabh.sharma7 at gmail.com
Thu Sep 16 17:38:14 EDT 2010


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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