Perl Option For Mir Target Prediction?

Question

[Krisr]

I have a few hundred sequences pulled from one perl script that I'd like to check for microrna binding motifs. I would like to run these sequences through the miranda program, which I can do here. However, I would like to have the perl script just take each sequences and run it through a prediction tool. Does anyone now of any perl implementations of microrna prediction tools?

Answer 1

[Ryan Thompson]

Last year, I wrote a perl wrapper for miRanda. You can find it among the scripts here.

There are two wrappers. One outputs in Genbank format, and the other outputs in CSV. The Genbank output can be used as input to the reporter script that produces nice HTML summary output.

Hope this helps.

Edit: The OP has pointed out to me that these scripts depend on some of my unpublished perl modules. I will eventually publish them on CPAN if they are worthy, or else I will rewrite my scripts not to use them. Until then, you can download them from my personal server here:

• http://mneme.dyndns.org/~ryan/Projects/Text-CSV-Euclid/Text-CSV-Euclid-0.103470.tar.gz
• http://mneme.dyndns.org/~ryan/Projects/IPC-Open3-System/IPC-Open3-System-0.110180.tar.gz

Obviously, I did not originally write this code with publishing in mind.

[Ryan Thompson]

By the way, note that this isn't a perl implementation of miRanda. It's a wrapper script. Hopefully that's good enough for you.