comRNA is a new program that predicts common RNA secondary structure motifs in a group of related sequences, developed by Yongmei Ji, Xing Xu and Gary Stormo at Washington University in Saint Louis.
It is an implementation of the algorithms described in the paper "A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences, Bioinformatics, 2004 Jul 10; 20(10):1591-1602.". The program is written in C++.
The algorithm applies graph-theoretical approaches to automatically detect common RNA secondary structure motifs in a group of functionally or evolutionarily related RNA sequences. The advantages of this method are that it:
does not require the presence of global sequence similarities (but can take advantage of it),
does not require prior structural alignment, and
is able to detect pseudoknot structures.