HXMATCHHxmatch computes the consensus structure including pseudoknots based on an alignment of a few RNA sequences. The algorithm combines thermodynamic and covariation information to assign scores to all possible base pairs, the base pairs are chosen with the help of the maximum weighted matching algorithm.
Download the source code of hxmatch (v1.2.1 gzipped tar file, last update Apr 9, 2008).
The man page.
Data and Results
Data - sequence and alignment data of sequences with pseudoknots
alpha-operon mRNA results.
Results for SRP RNA, tmRNA, RNase P RNA, Telomerase RNA and 16S rRNA based on database alignments
Results for the datasets used in ILM   [ Ruan et al., 2003 ]
for 5S rRNA, SRP RNA, tmRNA, Telomerase RNA and 16S rRNA based on database alignments
(including a comparison of the accuracy of ilm and hxmatch)
Prediction of consensus RNA structures including pseudoknots
Christina Witwer, Ivo L. Hofacker and Peter F. Stadler
IEEE/ACM Trans.Comp.Biol.Bioinf., 1: 66-77 (2004)
[abstract] [Postscript] [PDF]