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Bioinformatics. 2009 Apr 15;25(8):1080-1. doi: 10.1093/bioinformatics/btp095. Epub 2009 Mar 5.

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

Author information

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

Abstract

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.

PMID:
19269988
[PubMed - indexed for MEDLINE]
PMCID:
PMC2720711
Free PMC Article
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