[Bioperl-l] Handling miRNA's

[Chris Fields]

I don't think there's anything like this in Bioperl, and I'm unfamilar with
the naming scheme you're using.  If you're searching for specific miRNA's, a
good resource looks like the miRNA database, which seems to be updated
regularly (http://microrna.sanger.ac.uk/sequences/) and uses the same system
for RNA annotation that you use (which, I'm guessing, is a standardized
annotation scheme of some sort).  I believe the database is downloadable and
searchable by name, so you could probably build a querying scheme using LWP
or HTTP::Request (if the web interface allows for this).  I know that Sean
Eddy's Rfam database (http://www.sanger.ac.uk/Software/Rfam/) also has
information on miRNA's, but it's somewhat limited. 


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: Wednesday, February 08, 2006 3:45 PM
> To: 'bioperl-l'; bioperl-l-bounces at lists.open-bio.org
> Cc: James.R.Brown at gsk.com
> Subject: Re: [Bioperl-l] Handling miRNA's
> 
> 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
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
>