Profiling and searching for RNA pseudoknot structures in genomes

Authors:
Chunmei Liu;Yinglei Song;Russell L. Malmberg;Liming Cai
Affiliations:
Department of Computer Science, University of Georgia, Athens, GA;Department of Computer Science, University of Georgia, Athens, GA;Department of Plant Biology, University of Georgia, Athens, GA;Department of Computer Science, University of Georgia, Athens, GA
Venue:
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
Year:
2005

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Abstract

A new method is developed that can profile and efficiently search for pseudoknot structures in noncoding RNA genes. It profiles interleaving stems in pseudoknot structures with independent Covariance Model (CM) components. The statistical alignment score for searching is obtained by combining the alignment scores from all CM components. Our experiments show that the model can achieve excellent accuracy on both random and biological data. The efficiency achieved by the method makes it possible to search for the pseudoknot structures in genomes of a variety of organisms.