massachusetts institute of technology (mit)
computer science and artificial intelligence laboratory (csail)
theory of computation group (toc)
computation and biology group (compbio)
email queries email@example.com
MSARi is a program for detecting conservation of RNA secondary structure. It searches orthologous nucleotide sequences for statistically signficant variations conserving a candidate secondary structure. It is described in "MSARi: Multiple sequence alignments for statistical detection of RNA secondary structure", by Coventry, Kleitman and Berger, which has been appeared PNAS. (Proceedings of the National Academy of Sciences (2004) 101, no. 33: 12102-12107)
Download MSARi's source code here. We are still working on a more user-friendly release. Those that are interested in experimenting with MSARi themselves may find it helpful to examine the example code in the file MSARi/tests/general_test.py.Results for the MSARi scan of the EGO database are available in tarred, gzipped format here.