Family Classification Of Mirna

Question

[liran0921]

Dear everyone,

I have a list of miRNA and I want to cluster them into each miRNA family. I found this data file miFam.dat (http://www.mirbase.org/ftp.shtml) from miRBase which include the miRNA family information. But how can I use this data to classify my miRNA list. Thanks.

Merry Christmas and happy new year!

Answer 1

[Charles Warden]

I'm not familiar with that file.

TargetScan provides a pull-down of miRNA families for varying degrees of conservation (step #3). Perhaps that can help?

http://www.targetscan.org/

[liran0921]

thanks. But Targetscan seems to search the miRNA one by one, which will be too inefficient with a long list of miRNAs.

[Charles Warden]

I think there are a couple options:

1) Download the entire database as a text file

http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61

2) I thought you just wanted to know the families (and weren't actually interested in the targets). If this is the case, all you need to know if the names in the pull-down menu (for example, let-7/98/4458/4500 is a family with 4 miRNAs)

I agree that this may not be the most direct solution, but I thought it might be able to help

[liran0921]

Thanks! This is useful.