Question: miRNA target prediction tools
0
gravatar for Shahzad
4.0 years ago by
Shahzad10
Pakistan
Shahzad10 wrote:

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 Many softwares have become outdated and their webpages and download links are no longer functional. 

 

ADD COMMENTlink modified 14 months ago by Bade40 • written 4.0 years ago by Shahzad10
1
gravatar for Diego D.
4.0 years ago by
Diego D.40
Chile
Diego D.40 wrote:

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 COMMENTlink written 4.0 years ago by Diego D.40
1
gravatar for Vivek Todur
4.0 years ago by
Vivek Todur50
Bangalore
Vivek Todur50 wrote:

Hi,

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

psRNATarget: http://plantgrn.noble.org/psRNATarget/

Good Luck,

ADD COMMENTlink written 4.0 years ago by Vivek Todur50
1
gravatar for Bade
14 months ago by
Bade40
United States
Bade40 wrote:

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 COMMENTlink written 14 months ago by Bade40
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