Genomic Locations of Mature miRNA

[ilivyatan]

I'm interested in genomic locations of both precursor and mature microRNAs.
I'm familiar with mirBase which contains the sequences of both types that can be downloaded as fasta files, but I'm interested in more of a .bed type of file with genomic locations.
The available .gff's contain that information for microRNA precursors, but I can't find it for the mature mirs. When looking at a specific mir in the database the offset of the mature mir relative to the precursor sequence is provided so the information is there. I'm looking for a way to download it in bulk and not one by one.
Does anyone have any idea how to do this, or alternatively a reference to another database with easier access to this information.

I've already looked at UCSC - only precursors and fRNAdb - only sequences.

Appreciate the help!

[rafir]

Hello Ilivyan, I have the same question did you ever resolve this problem?

[Chirag]

Hi,

You can download the gff file of species, of your interest, from http://www.mirbase.org/ftp.shtml

To convert it into .bed format, u can simply do it from awk on your command line

cat FILENAME.gff | grep -v "#" | grep -v "^$" | sed 's/"/ /g' | awk '{ print "chr"$1"\t"$4"\t"$5"\t"$13"\t1000\t"$7 }' | sort -k1,1 -k2,2g > OUTPUT.bed


As far as mature miRNAs are concerned, i do not know the exact information. You could simple blast to get the position information, or write a small script.

cheers
Chirag

[skycreative]

so cool shell command

Hi,

You can download the gff file of species, of your interest, from http://www.mirbase.org/ftp.shtml

To convert it into .bed format, u can simply do it from awk on your command line

cat FILENAME.gff | grep -v "#" | grep -v "^$" | sed 's/"/ /g' | awk '{ print "chr"$1"\t"$4"\t"$5"\t"$13"\t1000\t"$7 }' | sort -k1,1 -k2,2g > OUTPUT.bed


As far as mature miRNAs are concerned, i do not know the exact information. You could simple blast to get the position information, or write a small script.

cheers
Chirag