Thank you very much.
I just realized the biomart server is up & running again. 
Now I have learnt that BioMart can extract a lot of data from Ensembl (from where I have been told to get the genes info)
and can also download the validated miRNAs compressed files.

I stress the main problem I am experienciing, though, is still open.
In fact I have to find a piece of data that allows me to relate all the gene info I can get from BioMart querying Ensembl 
to the downloaded miRNAs info. This is because the miRNA identifier is not available through BioMart .... I wish I were mistaken.

However, some other (unique ?) miRNA attribute, that is available through BioMart, is also present in the VALIDATED targets file that is downloadable in XLS format from miRecords. This piece of data would allow me to relate the gene 3UTS string to the targeting miRNA.
The issue is that I do not know how often such miRecords file is updated, and the downloading  is to be performed outside R environment.
Maybe R might handle the download automatically through the R "system" function and then the XLS file can be processed through R package
"RExcelInstaller" ..... just a speculation ...

Regards,
Maura 


-----Messaggio originale-----
Da: michael watson (IAH-C) [mailto:michael.watson@bbsrc.ac.uk]
Inviato: dom 28/06/2009 10.15
A: Steve Lianoglou
Cc: mauede@alice.it; Sean Davis; bioconductor List
Oggetto: RE: [BioC] R:  R: R: how to find the VALIDATED pair (miRNA, gene-3'UTR-sequence)
 
The power of Bioconductor :D

So, some code would look like this:

> mat <- gzcon(url("ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/mature.fa.gz"))
> matfas <- readFASTA(mat, strip.descs=TRUE)
> matstar <- gzcon(url("ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/maturestar.fa.gz"))
> matstarfas <- readFASTA(matstar, strip.descs=TRUE)


-----Original Message-----
From: Steve Lianoglou [mailto:mailinglist.honeypot@gmail.com]
Sent: Sun 28/06/2009 8:51 AM
To: michael watson (IAH-C)
Cc: mauede@alice.it; Sean Davis; bioconductor List
Subject: Re: [BioC] R:  R: R: how to find the VALIDATED pair (miRNA, gene-3'UTR-sequence)
 
> They'll be in fasta format, and whether or not Bioconductor can read  
> them in I have no idea - I use Bioperl for all my sequence handling.


Yes, bioconductor can: the Biostrings package provides readFASTA and  
writeFASTA that handle this for you.

-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

Contact Info: http://cbio.mskcc.org/~lianos











tutti i telefonini TIM!


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