Thank you so much for your suggestion. The student, who extracted and handled miRNA and target genes sequences before my take-over, states the following: miRNA sequences can be downloaded from: http://microrna.sanger.ac.uk/sequences/ Gene sequences can be download from: http://www.ensembl.org/index.html I see that such data can be downloaded in Fasta format pretty easily and stored into a text file that I can manipulate through an R script. The real problem for me (I am a newbie in this research field) is to know which miRNAs match which genes. The matching information can come from Biology experiments which mark the pair (miRNA, gene) as "validated". The matching information can also come from computational predictions which mark the pair as "predicted". The two sets above have a non-null intersection. The goal of our project is to maximize such an intersection, but also to increase the subset of the "predicted", not yet "validated", to help with Bilogists' experiments. In short, the label "predicted", "validated", or "none of the two cases", is very important to us. I cannot retrieve such information in the files dowloaded from http://microrna.sanger.ac.uk/sequences/ and http://microrna.sanger.ac.uk/cgi-bin/targets/v5/download.pl Maybe it's just my ignorance in this field that prevents me from reading out the information.. Anyway, also the student, who preceded me, experienced the same problem. To overcome ths hurdle he wrote a python script that downloads some HTML pages from http://mirecords.umn.edu/miRecords/ where the label "validated" and /or "predicted" is attached to the respective identifiers of the pair miRNA <--> target gene. Since I am familiar with R, I am not with python, I wonder whether there exist a s/w interface to access miRecords, which is callable from R scripts. ..... unless such pairs-link can somehow be retrieved from the dowloadable Fasta files or some other way ... Regards, Maura E tutti i telefonini TIM! [[alternative HTML version deleted]]

Check out our package CORNA, published in Bioinformatics this year: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/6/832 http://corna.sourceforge.net/ http://www.ncbi.nlm.nih.gov/pubmed/19181683 Thanks Mick -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of mauede at alice.it Sent: 17 June 2009 15:52 To: bioconductor at stat.math.ethz.ch Subject: [BioC] miRNA validated/predicted label Thank you so much for your suggestion. The student, who extracted and handled miRNA and target genes sequences before my take-over, states the following: miRNA sequences can be downloaded from: http://microrna.sanger.ac.uk/sequences/ Gene sequences can be download from: http://www.ensembl.org/index.html I see that such data can be downloaded in Fasta format pretty easily and stored into a text file that I can manipulate through an R script. The real problem for me (I am a newbie in this research field) is to know which miRNAs match which genes. The matching information can come from Biology experiments which mark the pair (miRNA, gene) as "validated". The matching information can also come from computational predictions which mark the pair as "predicted". The two sets above have a non-null intersection. The goal of our project is to maximize such an intersection, but also to increase the subset of the "predicted", not yet "validated", to help with Bilogists' experiments. In short, the label "predicted", "validated", or "none of the two cases", is very important to us. I cannot retrieve such information in the files dowloaded from http://microrna.sanger.ac.uk/sequences/ and http://microrna.sanger.ac.uk/cgi-bin/targets/v5/download.pl Maybe it's just my ignorance in this field that prevents me from reading out the information.. Anyway, also the student, who preceded me, experienced the same problem. To overcome ths hurdle he wrote a python script that downloads some HTML pages from http://mirecords.umn.edu/miRecords/ where the label "validated" and /or "predicted" is attached to the respective identifiers of the pair miRNA <--> target gene. Since I am familiar with R, I am not with python, I wonder whether there exist a s/w interface to access miRecords, which is callable from R scripts. ..... unless such pairs-link can somehow be retrieved from the dowloadable Fasta files or some other way ... Regards, Maura E tutti i telefonini TIM! [[alternative HTML version deleted]] _______________________________________________ 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