Question

miRNA target prediction tools

0

Entering edit mode

9.7 years ago

Shahzad ▴ 30

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 Many softwares have become outdated and their webpages and download links are no longer functional.

miRNA-target-prediction Virus virus-genome miRNA • 4.5k views

ADD COMMENT • link updated 2.6 years ago by Ram 44k • written 9.7 years ago by Shahzad ▴ 30

score 1 · Answer 1 · 2015-03-06

1

Entering edit mode

9.7 years ago

Diego D. ▴ 50

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!

ADD COMMENT • link 9.7 years ago by Diego D. ▴ 50

Ram · Answer 2 · 2015-03-06

1

Entering edit mode

9.7 years ago

Vivek Todur ▴ 60

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

ADD COMMENT • link updated 2.6 years ago by Ram 44k • written 9.7 years ago by Vivek Todur ▴ 60

score 1 · Answer 3 · 2017-12-29

1

Entering edit mode

6.9 years ago

Bade ▴ 40

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

ADD COMMENT • link 6.9 years ago by Bade ▴ 40