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Bioinformatics Advance Access originally published online on March 5, 2009
Bioinformatics 2009 25(8):1080-1081; doi:10.1093/bioinformatics/btp095
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

RNATOPS-W: a web server for RNA structure searches of genomes

Yingfeng Wang 1, Zhibin Huang 1, Yong Wu 1, Russell L. Malmberg 2,3 and Liming Cai 1,3,*

1Department of Computer Science, 2Department of Plant Biology and 3Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA

*To whom correspondence should be addressed.


  Abstract

Summary: RNATOPS-W is a web server to search sequences for RNA secondary structures including pseudoknots. The server accepts an annotated RNA multiple structural alignment as a structural profile and genomic or other sequences to search. It is built upon RNATOPS, a command line C++software package for the same purpose, in which filters to speed up search are manually selected. RNATOPS-W improves upon RNATOPS by adding the function of automatic selection of a hidden Markov model (HMM) filter and also a friendly user interface for selection of a substructure filter by the user. In addition, RNATOPS-W complements existing RNA secondary structure search web servers that either use built-in structure profiles or are not able to detect pseudoknots. RNATOPS-W inherits the efficiency of RNATOPS in detecting large, complex RNA structures.

Availability: The web server RNATOPS-W is available at the web site www.uga.edu/RNA-Informatics/?f=software&p=RNATOPS-w. The underlying search program RNATOPS can be downloaded at www.uga.edu/RNA-Informatics/?f=software&p=RNATOPS.

Contact: cai{at}cs.uga.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Ivo Hofacker

Received on November 5, 2008; revised on February 15, 2009; accepted on February 16, 2009

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