Mirna Target Prediction In Dog Genome

Question

[neal.platt]

I have a few hundred potential miRNAs as predicted by miRanalyzer for the dog genome. I am interested in finding proteins/potential binding sites. Software that I have found online either (A) only takes a single miRNA as input or (B) is designed with specific species (human, mouse, Drosophila) in mind. Does anyone have a reccomendation for miRNA target prediction that can handle an input file containing a thousand sequences?

Answer 1

[Rm]

Check list of MicroRNA target prediction tools available: http://www.exiqon.com/microrna-target-prediction Some of them can be run locally (I haven't tested though)

[neal.platt]

Thanks for the link. I have actually looked through those and am trying to figure out how to adapt them to my data set. Thanks.

[Rm]

Try http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html : it takes multiple sequences at a time: you can upload your target sequences (from dog genome) and query mirna sequences