Predict miRNA targets using multiple prediction algorithms

Question

[nathanielsaxe]

I came across this set of perl scripts that take the output of miranda, pita and RNAhybrid and compares the output to determine the "best" mirna target. It takes one mRNA and compares it to a database of miRNAs, I was thinking of doing the reverse, where I have one miRNA and see which mRNAs in a list the miRNA targets.

Does anyone know where I can find something like this?

Thanks

Answer 1

[aheinzel]

miRWalk2.0 should be able to do both by either starting from a set of mRNAs or miRNAs and provides the option to use multiple prediction algorithms.

[nathanielsaxe]

Is it possible to use a custom set of miRNA and mRNA sequences? Forgot to add that part.

[Lorena Pantano]

Hi,

if you have custom mRNA sequences, then you don't have more options that run this several time. I don't know any tool that can work with custom in both side.

I worked several times with custom miRNA sequences and use targetScanCustom. And although you can create the custom mRNA files, I used always the compiled DB they provide with 3' UTR.

If your species is a plant, I think you have more options.