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The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
Department of Biomolecular Engineering and the UCSC RNA Center, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA 1Division of Biological Sciences, Cell and Developmental Biology Section and Center for Molecular Genetics, University of California at San Diego La Jolla, CA 92093, USA
*To whom correspondence should be addressed. Tel: +1 831 459 1511; Fax: +1 831 459 3139; Email: lowe{at}soe.ucsc.edu
Received January 12, 2005. Revised February 28, 2005. Accepted February 28, 2005.
Transfer RNAs (tRNAs) and small nucleolar RNAs (snoRNAs) are two of the largest classes of non-protein-coding RNAs. Conventional gene finders that detect protein-coding genes do not find tRNA and snoRNA genes because they lack the codon structure and statistical signatures of protein-coding genes. Previously, we developed tRNAscan-SE, snoscan and snoGPS for the detection of tRNAs, methylation-guide snoRNAs and pseudouridylation-guide snoRNAs, respectively. tRNAscan-SE is routinely applied to completed genomes, resulting in the identification of thousands of tRNA genes. Snoscan has successfully detected methylation-guide snoRNAs in a variety of eukaryotes and archaea, and snoGPS has identified novel pseudouridylation-guide snoRNAs in yeast and mammals. Although these programs have been quite successful at RNA gene detection, their use has been limited by the need to install and configure the software packages on UNIX workstations. Here, we describe online implementations of these RNA detection tools that make these programs accessible to a wider range of research biologists. The tRNAscan-SE, snoscan and snoGPS servers are available at http://lowelab.ucsc.edu/tRNAscan-SE/, http://lowelab.ucsc.edu/snoscan/ and http://lowelab.ucsc.edu/snoGPS/, respectively.
Correspondence may also be addressed to Peter Schattner. Email: schattner{at}soe.ucsc.edu
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