Iterative Loop Matching (ILM)

An Approach to the Prediction of RNA Secondary Structures with Pseudoknots

Jianhua Ruan and Weixiong Zhang
Department of Computer Science and Department of Genetics
Washington University in St. Louis, St. Louis, MO 63130, USA
email: {jruan,zhang}@cse.wustl.edu; (314)935-8788; Fax:(314)935-7302

Iterative loop matching (ILM) is an extended dynamic programming algorithm that is able to predict RNA secondary structures including pseudoknots. ILM can not only predict consensus structures for aligned homologous sequences, using combined thermodynamic and covariance scores, but can also be applied to individual sequences, using thermodynamic information alone.

The method is implemented in ANSI C and can be freely downloaded here (gzipped tar file). See the README file for details.

Online Web server for ILM and weighted matching methods for RNA secondary structures with pseudonots is here.

To learn more about the method, take a look at a preprint version of the paper describing the method (pdf).

Supplementary Materials