Skip Navigation

Nucleic Acids Research 2005 33(Web Server Issue):W686-W689; doi:10.1093/nar/gki366
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (228K) Freely available
Right arrow Screen PDF (178K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Schattner, P.
Right arrow Articles by Lowe, T. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Schattner, P.
Right arrow Articles by Lowe, T. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

Peter Schattner, Angela N. Brooks1 and Todd M. Lowe*

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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Gen Biol EvolHome page
X. Chen, L. J. Collins, P. J. Biggs, and D. Penny
High Throughput Genome-Wide Survey of Small RNAs from the Parasitic Protists Giardia intestinalis and Trichomonas vaginalis
Gen Biol Evol, July 24, 2009; 2009(0): 165 - 175.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
M. de Planell-Saguer, D. G. Schroeder, M. C. Rodicio, G. A. Cox, and Z. Mourelatos
Biochemical and genetic evidence for a role of IGHMBP2 in the translational machinery
Hum. Mol. Genet., June 15, 2009; 18(12): 2115 - 2126.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
S. Paredes and K. A. Maggert
Expression of I-CreI Endonuclease Generates Deletions Within the rDNA of Drosophila
Genetics, April 1, 2009; 181(4): 1661 - 1671.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
W. A. Decatur and M. N. Schnare
Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs
Mol. Cell. Biol., May 15, 2008; 28(10): 3089 - 3100.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
T. Mourier, C. Carret, S. Kyes, Z. Christodoulou, P. P. Gardner, D. C. Jeffares, R. Pinches, B. Barrell, M. Berriman, S. Griffiths-Jones, et al.
Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum
Genome Res., February 1, 2008; 18(2): 281 - 292.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Piekna-Przybylska, W. A. Decatur, and M. J. Fournier
The 3D rRNA modification maps database: with interactive tools for ribosome analysis
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D178 - D183.
[Abstract] [Full Text] [PDF]

Home page
 Genes Dev.Home page
M. G. Smith, T. A. Gianoulis, S. Pukatzki, J. J. Mekalanos, L. N. Ornston, M. Gerstein, and M. Snyder
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis
Genes & Dev., March 1, 2007; 21(5): 601 - 614.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. M. Goodenbour and T. Pan
Diversity of tRNA genes in eukaryotes
Nucleic Acids Res., December 4, 2006; 34(21): 6137 - 6146.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T.-H. Chang, H.-D. Huang, T.-N. Chuang, D.-M. Shien, and J.-T. Horng
RNAMST: efficient and flexible approach for identifying RNA structural homologs.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W423 - W428.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.