miRNA target prediction tools

Question

[Shahzad]

hi,

I want to predict miRNAs(Plants) targets in a virus genome. I have tried many tools but most of them are specific for a few species like human, rat etc. I have succeeded to analyse this task by RNAhybrid and miRanda uptil now. Anyone know which other tool can do this analysis. Many softwares have become outdated and their webpages and download links are no longer functional.

Answer 1

[Diego D.]

Hi Shzad,

Most softwares search for host miRNA targets. Anyway, there are several toos for miRNAs target prediction that you could use.

Vita

http://vita.mbc.nctu.edu.tw/

TargetScan

http://www.targetscan.org/

VIRmirRNA

http://crdd.osdd.net/servers/virmirna/

Good luck!

Answer 2

[Vivek Todur]

Hi,

Try psRNATarget server for target identification analysis. which has huge inbuilt library for target search, but also supports for uploading user defined sequences.

Good Luck

Answer 3

[Bade]

Hi Shahzad,

Although late, but I would like to add sPARTA that we use in our lab. It is very good for whole genome target discovery.

sPARTA: https://github.com/atulkakrana/sPARTA

Bade