Journal Article

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

Yingfeng Wang, Zhibin Huang, Yong Wu, Russell L. Malmberg and Liming Cai

in Bioinformatics

Volume 25, issue 8, pages 1080-1081
Published in print April 2009 | ISSN: 1367-4803
Published online March 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp095
RNATOPS-W: a web server for RNA structure searches of genomes

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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@cs.uga.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1423 words. 

Subjects: Bioinformatics and Computational Biology

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