Thank you so much. Sorry for my basic questions that must read very silly for Biologists. As a physicist I was supposed to help Biology research with physics facets (free energy minimization, Molecular Dynamics, and so on). Unluckily, the student in charge of providing the test data (miRNA sequences and target gene sequences) has unexpectedly dropped out of the school just a few weeks from his Ms. thesis defence ! Consequently each member of the research group is getting a bigger slice of the pie ...
The problem is that we have to make the database interrogation (data path selection) and data extraction processes fully automatic. miiRecords is searchable interactively through selecting items from some menus hierarchily structured.. That's why the drop-out student wrote some Python code to automatically extract miRNAa and gene sequences. Therefore my question is: how can I interrogate and extract data from miRecors, or any of the databases you suggested, automatically ? Is there any standard s/w interface whose functions are callable from a <...> program (which language is the most appropriate ? Thank you so much. Kind regards, Maura -----Messaggio originale----- Da: iaingallag...@btopenworld.com [mailto:iaingallag...@btopenworld.com] Inviato: mar 16/06/2009 21.53 A: mau...@alice.it Cc: r-h...@stat.math.ethz.ch Oggetto: Re: [R] R and miRecords Try TargetScan, Pictar, miRbase. These are all useful miRNA databases. Data can be downloaded as cvs or tab delimited files and parsed in R after that. In fact this may be possible with the resource you have looked at (although I haven't checked). Cheers Iain --- On Tue, 16/6/09, David Winsemius <dwinsem...@comcast.net> wrote: From: David Winsemius <dwinsem...@comcast.net> Subject: Re: [R] R and miRecords To: mau...@alice.it Cc: r-h...@stat.math.ethz.ch Date: Tuesday, 16 June, 2009, 4:24 PM Looks like a BioConductor question. On Jun 16, 2009, at 11:05 AM, <mau...@alice.it> wrote: > I wonder whether R provides an interface to access miRecords data. > Particularly, I am looking for extracting humans miRNA and target genes > sequences. > All such information is stored in there in a set of structured web site > pages (http://mirecords.umn.edu/miRecords) > I would greatly appreciate any suggestion even about other data bases from > where it is possible to get the same sort of data. > I had a look at the database whose interface is provided by the Bioconductors > package. It seems to have a diferent contents, though. > > Thank you in advance, > Maura > > > tutti i telefonini TIM!de. David Winsemius, MD Heritage Laboratories West Hartford, CT ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. tutti i telefonini TIM! [[alternative HTML version deleted]]
______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
