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- Title
RNATOPS-W: a web server for RNA structure searches of genomes.
- Authors
Yingfeng Wang; Zhibin Huang; Yong Wu; Russell L. Malmberg; Liming Cai
- 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響ᾷګ 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.
- Publication
Bioinformatics, 2009, Vol 25, Issue 8, p1080
- ISSN
1367-4803
- Publication type
Academic Journal
- DOI
10.1093/bioinformatics/btp095