miRNA target prediction

Question

[vidyamurthy28]

Hi,

Please help

I am working on abiotic stress plant miRNAs.

I have designed primers for miRNAs and now want to study targets for those miRNA.

My question is : when we run a FASTA sequence of a miRNA on the target prediction tool, the result what we get is say 30 targets.( which have the same function but have different alignment)

So how do we pick the target among the 30 specific to the stress?

[Ram]

You might wanna provide some examples to get better answers.

At a cursory glance, I'd say you might have to use a combination of setting more stringent BLAST parameters and picking the match with better identity and lower e-value. Species match and phylogenetic distance might also be taken as contributing factors.

[Renesh]

miRNA will be complimentary to target. The identity is not important here. As he is working on plant, there should be no complimentary between 9-11 bases for good target.

[Ram]

Oh. I was thinking of BLAST matches in general WRT that suggestion. I'm not a plant person, so I apologize for any mistaken assumptions.

Answer 1

[Renesh]

You need to consider the parameter like central mismatch in miRNA, energy to unpair target site and the tendency to form secondary stem loop structure.

Answer 2

[Chirag Nepal]

As you said, you have target tools, those tools probably give some sort of score, try to make use of that score and have a look at top hits. You also said, you have about 30 genes, then read that are assigned/putative functions of those genes, and check if they have known functions related to stress or not.

In general, use target prediction tools and have a look at prediction (high) scores.

Answer 3

[Bade]

You might want to generate some PARE (Parallel analysis of read ends) data and use tools like sPARTA

Here is the link to full paper.

If you can't generate PARE data, then predict targets, check sPARTA readme on how to do that, and sort them on least to high penalty score. Take top 10 for your downstream analysis, and yes keep your fingers crossed.

Bade