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RNATOPS-W: A Web Server for RNA Structure Searches of Genomes
BibTeX
@MISC{Wang_rnatops-w:a,
author = {Yingfeng Wang and Zhibin Huang and Yong Wu and Russell L. Malmberg and Liming Cai},
title = {RNATOPS-W: A Web Server for RNA Structure Searches of Genomes},
year = {}
}
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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:
