Question: Mirna Target Prediction
5
gravatar for Janake
6.2 years ago by
Janake160
United States
Janake160 wrote:

I am trying to predict targets for miRNA. The potential targets are ESTs derived from 454 sequencing and the species of interest (a non-model insect) doesn’t have an annotated genome. I am planning to use Targetspy program (http://www.targetspy.org/). The problem that I have is how do I predict the 3’ utrs from the EST sequences? I would appreciate your thoughts.

utr mirna target • 2.0k views
ADD COMMENTlink modified 3.4 years ago by julierey520 • written 6.2 years ago by Janake160
1

I think you should start by predicting ORFs in the ESTs, when you'll have them you'll get the UTRs

ADD REPLYlink written 6.2 years ago by Asaf4.8k

To further Asaf's point -- are your ESTs likely to be whole transcripts?

ADD REPLYlink written 6.2 years ago by Qdjm1.9k

Thanks for your comments Asaf and Qdjm. ORF prediction is a good suggestion. However, most of the sequences may not be whole transcripts as they are derived from 454 data.

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Janake160

I wouldn't confound the target prediction with another imperfect prediction. Afaik (lacking a tidbit of evidence), miRNAs do not only target 3'UTRs but can target anywhere on the mRNA. As a conclusion the UTR/ORF prediction is not beneficial.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Michael Dondrup44k

I'm at a similar place with my miRNA research - trying to predict targets for a non-model insect using 454 sequencing reads. Did you find a way to do this?
 

ADD REPLYlink written 3.4 years ago by julierey520
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1485 users visited in the last hour