[BioC] Small RNAs database

Sean Davis sdavis2 at mail.nih.gov
Fri Jul 11 12:43:25 CEST 2008

On Fri, Jul 11, 2008 at 6:01 AM, Daniel Brewer <daniel.brewer at icr.ac.uk> wrote:
> Hi,
> Not strictly bioconductor related, so apologies, but I was wondering
> whether anyone knew of a good all encompassing small RNAs database.  I
> would like to find all small RNAs (RNAis etc.) within a particular
> genomic region.

I would take a look at the UCSC genome browser track for small RNAs,
which includes snoRNAs as well as miRNAs (and a few others).  I do not
know of another resource that combines all the data this way.  It is
quite easy to make a custom track that includes your regions of
interest and to then extract using the table browser the information
that overlaps your custom track.  Alternatively, you can download the
entire track (I think it is the wgRNA table, if I remember correctly)
and process in R.


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