Are There Python Packages That Do Rna-Rna Interaction Prediction?

Question

[ericmajinglong]

Does anybody know if there are any Python packages that can be used for RNA-RNA interaction prediction? Specifically, I am looking to scan 15-mer windows of a sequence to see if it can hybridize to a different target sequence.

[Pierre Lindenbaum]

please don't cross-post ( http://stackoverflow.com/questions/19059946 ) and validate or comment the answers you already received http://www.biostars.org/show/user/7576

Answer 1

[Rnomics]

there are 2 series of tools from Freiburg and Vienna, see the details of the documentation depending on what you want to do exactly: Freiburg RNA tools: http://rna.informatik.uni-freiburg.de:8080 Vienna Package: http://www.tbi.univie.ac.at/RNA/

[ericmajinglong]

Specifically, what I would like to do is to know the Tm and other thermodynamic parameters (latter if possible), as well as a prediction of the base pairing sites. I think the IntaRNA package can accomplish this, but it requires the Vienna RNA package. Unfortunately, I have had errors installing the Vienna RNA package, with the following errors:

ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation)