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Bioinformatics Advance Access published online on March 5, 2009
Bioinformatics, 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, University of Georgia, Athens, GA 30602.
2Department of Plant Biology, University of Georgia, Athens, GA 30602
3Institute of Bioinformatics, University of Georgia, Athens, GA 30602.

*To whom correspondence should be addressed. Dr. Liming Cai, E-mail: cai{at}cs.uga.edu


  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 (Huang et al., 2008), 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 an 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 website 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@cs.uga.edu

Supplementary Material: The online SUPPLEMENTARY MATERIAL contains additional experimental data.

Associate Editor: Prof. Ivo Hofacker

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

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