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. Sorry for my naive question. I am a physics postdoc... just jumped in the middle of a BioInformatic project. Thank you very much in advance, Maura Edelweiss tutti i telefonini TIM! [[alternative HTML version deleted]]

On Wed, Jun 17, 2009 at 8:08 AM, <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. > Looks like there is a download link on the home base of miRecords that gives you an excel spreadsheet. > > 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. > mirBase (http://microrna.sanger.ac.uk/) is perhaps the largest? Again, mirBase offers downloads of tab-delimited text files. > > Sorry for my naive question. I am a physics postdoc... just jumped in the > middle of a BioInformatic project. > > Thank you very much in advance, > Maura Edelweiss > > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > [[alternative HTML version deleted]]

mauede at 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

-----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Wacek Kusnierczyk Sent: Wed 6/17/2009 4:01 PM To: mauede at alice.it Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] miRNA and validated/predicted target genes mauede at 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

CORNA gets it's miRNA target information either from miRBase targets or microRNA.org - however, you can load any data you want into it. The confirmed microRNA targets database I know about is Tarbase: http://diana.cslab.ece.ntua.gr/tarbase/ I'm sorry if I misread your intentions - CORNA works downstream of microRNA:gene target prediction, it relies on other software and/or databases to do that. However, if you simply want to read data from miRBase into R, then CORNA can do that. Thanks Mick -----Original Message----- From: mauede@alice.it [mailto:mauede@alice.it] Sent: Thu 18/06/2009 4:04 AM To: michael watson (IAH-C); Michal Okoniewski; Wacek Kusnierczyk Cc: bioconductor at stat.math.ethz.ch Subject: R: [BioC] miRNA and validated/predicted target genes 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 at stat.math.ethz.ch] On Behalf Of Michal Okoniewski Sent: 17 June 2009 15:26 To: Wacek Kusnierczyk; mauede at alice.it Cc: bioconductor at 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 at alice.it Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] miRNA and validated/predicted target genes mauede at 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 at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e tutti i telefonini TIM! Vai su http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer