[BioC] R: R: R: how to find the VALIDATED pair (miRNA, gene-3'UTR-sequence)

[michael watson (IAH-C)]

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 at gmail.com]
Sent: Sun 28/06/2009 8:51 AM
To: michael watson (IAH-C)
Cc: mauede at 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