[Bioperl-l] Handling miRNA's

[Chris Fields]

Sorry if this gets posted twice.

Are you talking about sequences or text output from a specific program?  If
you are talking about sequences in a particular format, then Brian's right.
If you are talking about output, then we need to know which program you're
using, as a parser may exist, or prbably could be built from and existing
one.

There are a few modules in Bio::Tools that handle RNA (like QRNA,
tRNAscan-SE), so check those out first.  I'm currently finishing up a
Bio::Tools module for RNAMotif and have plans for making an ERPIN parser.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> barry.m.dancis at gsk.com
> Sent: Tuesday, February 07, 2006 2:26 PM
> To: bioperl-l; bioperl-l-bounces at lists.open-bio.org
> Subject: Re: [Bioperl-l] Handling miRNA's
> 
> It's the parser in particular that I need
> 
> 
> 
> 
> "Brian Osborne" <osborne1 at optonline.net> Sent by: 
> bioperl-l-bounces at lists.open-bio.org
> 07-Feb-2006 12:05
>  
> To
> barry.m.dancis at gsk.com, "bioperl-l" <bioperl-l at bioperl.org>, 
> bioperl-l-bounces at lists.open-bio.org
> cc
> 
> Subject
> Re: [Bioperl-l] Handling miRNA's
> 
> 
> 
> 
> 
> 
> Barry,
> 
> If the sequence information is in one of the formats that 
> Bioperl understands (Genbank, Swissprot flat, and so on) then 
> the answer is yes.
> This assumes that the details on sequence that you mentioned 
> are found in some sequence feature section in the file. But 
> it looks to me like there's no specialized parser for miRNA 
> sequence per se, I'll be corrected if I'm wrong.
> 
> Brian O.
> 
> 
> On 2/6/06 12:17 PM, "barry.m.dancis at gsk.com" <barry.m.dancis at gsk.com>
> wrote:
> 
> > Hi --
> > 
> >         Are there any classes for manipulating miRNA's with 
> functions
> such
> > as parsing the name, storing and interlinking pri/pre/mat sequences,
> etc?
> > 
> > Thanks,
> > 
> > Barry
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