[Bioperl-l] Handling miRNA's

[barry.m.dancis at gsk.com]

Hi Chris--

        The problem I am solving is given a mature miRna name, how do I 
use it to search for its pre/pri miRna and vice versa. For example, how to 
go from mir-102a* to hsa-mir-102a-1*. Yes, I can write a parser for it, 
but I'm hoping that someone else has already done it and has some bells 
and whistles to go with it.  Below is a hierarchy chart of a data 
structure to hold the naming information. The parsing is not trivial and 
given data in that structure there could be all kinds of neat functions 
that return various aspects of the names.

Barry












"Chris Fields" <cjfields at uiuc.edu> 
Sent by: bioperl-l-bounces at lists.open-bio.org
07-Feb-2006 17:40
 
To
barry.m.dancis at gsk.com, "'bioperl-l'" <bioperl-l at bioperl.org>
cc

Subject
Re: [Bioperl-l] Handling miRNA's






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

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
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
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