How to increase the speed of miRanda target prediction program?

Question

[lakhujanivijay]

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.

[Nicolas Rosewick]

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 ?

[Buffo]

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

[kuttibiotech2009]

I have installed miRanda tool. Can u help me to get the target genes?

[kuttibiotech2009]

what are the files required to run this tool... I have only expressed miRNA sequence file. what else do we need? where to download it?

Thanks in advance

[Nicolas Rosewick]

Check doc : https://cbio.mskcc.org/miRNA2003/src/miRanda-latest/man/miranda.html

From doc : miRanda reads RNA sequences (such as microRNAs) from file1 and genomic DNA/RNA sequences from file2. Both of these files should be in FASTA format.

[kuttibiotech2009]

Thank you sir, its helped a lot

[kuttibiotech2009]

My species name is Anas platyrhynchos.

Could you please tell me how to download the entire 3' UTR sequence?

Thank you in advance