[BioC] Is there a way of counting a miRNA binding sites in a target gene

[michael watson (IAH-C)]

I am not sure this information is stored within Ensembl at all.

Our package CORNA:

http://bioinformatics.iah.ac.uk/software/corna
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp059
http://corna.sourceforge.net/

Can read miRBase targets version 5, which should tell you where the predicted binding site is between the miR and the Ensembl gene

Mick

________________________________________
From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sean Davis [seandavi at gmail.com]
Sent: 09 February 2010 19:23
To: mauede at alice.it
Cc: Bioconductor List
Subject: Re: [BioC] Is there a way of counting a miRNA binding sites in a       target gene

On Tue, Feb 9, 2010 at 11:39 AM,  <mauede at alice.it> wrote:
> Is it possible to query BiomaRt and get the number of binding sites of a miRNA with a target gene ?
> I believe the coordinates of each binding site can be extracted as well. Which attributes shall I provide to
> extract such information, if any ?

Hi, Maura.  Have you had a look at the Ensembl Mart web portal?  You
can start there to see what is available via biomaRt.  If you have
questions after taking a look, let us know.

Sean

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