RNACAD stochastic context-free grammar system

RNACAD is a stochastic context-free grammar(SCFG) RNA modeling package that accounts for both primary and secondary structure information. SCFGs are roboust and allow arbitrary deviations from a pattern. One of its primary features is the use of a constraint system that increases its running performance considerably allowing large problems to be solved efficiently.

If you want to search for known RNA structure and produce multiple alignments of it with the consideration that some hits might only be distantly related, then this package might be the answer. Starting the tRNA tutorial is probably the quickest way to see what the system is capable of.

• See the tRNA tutorial
• See the README.txt for RNACAD.
• See the INSTALL.txt for RNACAD.

• rnacad-1.1.1.tar.gz
Package implementing stochastic context-free grammar modeling for RNA secondary structure modeling. Includes an end-to-end tutorial for simple t-RNA modeling.