Is there a program for finding secondary strutural RNA elements? - finding secondary strutural RNA elements (Sep/06/2005 )

Hello anyone,

I want to find secondary strutural elements in a mfold output file.
Is their a program that can convert e.q ct-file in a list of strutural elements.
Not just a RNA struture Viewer.

Thanks.

-MvIterson-

Hi

maybe mfold software can help you :
http://www.bioinfo.rpi.edu/applications/mfold/

extract :
Michael Zuker, professor of mathematical sciences, develops tools for predicting the secondary structure of RNA and DNA, mainly by using thermodynamic methods.
fred

Applications:

* RNA Folding
* DNA Folding
* Nucleic Acid Quikfold
Fold many RNA or DNA sequences at once. Simple output.
* Zipfold server
Minimum free energies only for many RNA or DNA sequences.
* Tm server
Compute minimum folding energies and Tm only for many RNA or DNA sequences.
* 2-state hybridization server
Compute free energy and Tm for the hybridization of two RNA or DNA sequences.
* Free Energy Determination
Given a secondary structure, compute its free energy.

-fred_33-

Try this: http://exon.umdnj.edu/software/RSmatch/

-cyberpostdoc-