Question: How to increase the speed of miRanda target prediction program?
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gravatar for Vijay Lakhujani
17 months ago by
Vijay Lakhujani4.0k
India
Vijay Lakhujani4.0k wrote:

I am running miRanda for miRNA target prediction and I noticed that its way too slow even when running on cluster with 60 cores. Any existing method or probable/possible suggestion/method/advice apart from this that could speed up the process? Did anybody try using GNU parallel, if yes I wanted to know how its being done.

mirna parallel miranada • 630 views
ADD COMMENTlink written 17 months ago by Vijay Lakhujani4.0k

I uses miRanda some time ago and it was ok in terms of speed (it was ~10 putative miRNA sequences against all cDNA sequences (~35.000 sequences)). In my memory it was like a couple of hours..

Could you explain your setup please ? and also the computational time ?

ADD REPLYlink modified 17 months ago • written 17 months ago by Nicolas Rosewick7.5k

agree, I have used it to predict targets for about 500 miRNAs and it doesn´t take more than 1 hour..

ADD REPLYlink written 17 months ago by Buffo1.5k
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