I browsed through your paper. It looks like CORNA is not another pair (miRNA - target gene) prediction program like miRANDA and so on ... ? If I am guessing right (am I ... ?) then what is CORNA basing its miRNA -target_gene affinity score on ? In my mind I have the three phases that miRANDA uses to score such "affinity". Phase-1 implements some empirical Biology rules, phase-2 implements free energy minimization, phase-3 implements conservation of species. Each phase is a finer screening that assigns a score to the target match. The final score is the total. I cannot understand which criteria (empirical or computational) are at the base of CORNA assessment. Is it a synthesis of the predictions of the many programs like miRANDA (for instance many are referred in miRecords). How is the (miRNA-target_gene) prediction, from computational programs like miRANDA, accounted for by CORNA ? How is the biologists' (miRNA-target_gene) validation accounted for by CORNA ? I read it uses a number of statistical tests but I cannot figure out which data the statistics is applied to ... maybe because I am not familiar with the information stored in the databases mentioned in the paper. Thank you. Kind regards, Maura -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Michal Okoniewski Sent: 17 June 2009 15:26 To: Wacek Kusnierczyk; mauede@alice.it Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] miRNA and validated/predicted target genes -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Wacek Kusnierczyk Sent: Wed 6/17/2009 4:01 PM To: mauede@alice.it Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] miRNA and validated/predicted target genes mauede@alice.it wrote: > I posted the following question to R mailing-list and was adviced to contact the BioConductors team. > > I have to find humans miRNA sequences and the correspondent validated and/or predicted gene sequences. > The only database I know of is http://mirecords.umn.edu/miRecords where all such information is accessed through a set of structured web site pages. > I wonder whether R or C++ provides an interface to automatically extract such data from miRecords or any other similar database. > > I would greatly appreciate any suggestion even about other databases from where it is possible to get the same sort of data and s/w packages that facilitate database access. > > alternatively to mirecords, you can download fasta-formatted human (and other) mirs and targets from mirbase at sanger [1], and importing fasta to r should be an easy task for you. alternatively, there are database dumps available. i don't know of an r/bioc package targetted specifically at a mirna database; it's possible that the data are not available for programmatic access otherwise than through a bulk download (or html parsing, if you prefer...) vQ [1] http://microrna.sanger.ac.uk ================== I played with miRGen : http://www.diana.pcbi.upenn.edu/cgi-bin/miRGen/v3/Targets.cgi#Results (quite comprehensive, seems to include miranda and several other target databases) and TargetScan: http://www.targetscan.org/ but as Wacek wrote - there's no biomaRt-like interface (at least I did not see...) but a lot of fun with html/flat file parsing instead :) Cheers, Michal _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor tutti i telefonini TIM! [[alternative HTML version deleted]]