Chapter category: RNA
Computational Gene-Finding for Noncoding RNAs
Noncoding RNAs: Molecular Biology and Molecular Medicine
Edited by: Jan Barciszewski and Volker A. ErdmannISBN: 0-306-47835-8
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Chapter authors:
Peter Schattner
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Computer gene-finding programs have been quite successful at locating protein-coding genes in both prokaryotic and eukaryotic genomes. However these programs—which use genomic features such as long open-reading-frames and codon signatures—are not designed to identify non-coding RNA (ncRNA) genes. As a result ncRNA-specific gene-finders have been required.
The first successful attempts at computational ncRNA gene-finding focussed on ncRNAs with well-characterized primary sequences and/or secondary structures, such as tRNAs or methylation-guide snoRNAs. In addition user-configurable RNA-motif search programs were developed. These programs search for RNAs by looking for user-specified primary-sequence motifs and stable secondary-structures as indicated by increased Watson-Crick base-pairing or low calculated free energies. However, to date, these RNA-motif searching programs have had only modest success at finding ncRNAs.
Recently, computational ncRNA gene-finders have been developed which show promise of locating a much larger number of previously undetected ncRNAs. Some of the most successful are based on comparative sequence analysis between genomes of related species. Others exploit base-composition signatures of ncRNAs or use new methods for RNA sequence alignment and secondary-structure prediction. With these approaches, numerous previously undetected ncRNAs have been predicted and subsequently experimentally confirmed in species including and the hyperthermophiles Methanococcus jannaschii and Pyrococcus furiosus.
This chapter will review the strategies employed in the principal computational ncRNA gene-finders. We will compare the successes of the different approaches as well as their limitations. Finally, we will consider the impact that these new computational methods are having on our picture of the world of ncRNAs.
Peter Schattner
Center for Biological Sciences and Engineering
University of California
Santa Cruz, California, U.S.A.
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