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@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Sean Davis [seandavi@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 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor