[Bioperl-l] How to find secondary structures

Tue May 25 16:38:12 UTC 2010

Yes, that would look for Rfam-based conserved structures.   Should work for the latest infernal release, but let me know if you run into problems.

Should also look at ERPIN and RNAMotif (both have similar BioPerl wrappers). 

chris

On May 25, 2010, at 11:20 AM, Mark A. Jensen wrote:

> Sounds like a job for infernal and it's Bioperl wrapper (in Bio::Tools::Run); right Chris?
> MAJ
> ----- Original Message ----- From: "Dubi Eldor" <dueldor at yahoo.com>
> To: <bioperl-l at bioperl.org>
> Sent: Tuesday, May 25, 2010 8:30 AM
> Subject: [Bioperl-l] How to find secondary structures
> 
> 
>> Hi,
>> 
>> I am a new user of BioPerl.
>> I would like to find secondary sturctures in sequences of ~10K nt long.
>> Are there any functions that can help me?
>> 
>> Thanks,
>> Dubi
>> 
>> 
>> 
>> 
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