Summary: October 5, 2007 23:2 WSPC - Proceedings Trim Size: 9.75in x 6.5in apbc018a
Finding non-coding RNAs through genome-scale clustering
Huei-Hun Tseng1, Zasha Weinberg2, Jeremy Gore2, Ronald R. Breaker2,3,4 and Walter L.
Departments of 1Computer Science and Engineering and 5Genome Sciences
University of Washington,
Seattle, WA 98105, USA
2Department of Molecular, Cellular and Developmental Biology, 3Howard Hughes Medical
Institute, 4Department of Molecular Biophysics and Biochemistry
New Haven, CT 06520-8103, USA
Non-coding RNAs (ncRNAs) are transcripts that do not code for proteins. Recent find-
ings have shown that RNA-mediated regulatory mechanisms influence a substantial por-
tion of typical microbial genomes. We present an efficient method for finding potential
ncRNAs in bacteria by clustering genomic sequences based on homology inferred from
both primary sequence and secondary structure. We evaluate our approach using a set
of Firmicutes sequences, and the results show promise for discovering new ncRNAs.