title: RNATOPS-W: a web server for RNA structure searches of genomes.
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.
authors.affiliation: Department of Computer Science, Department of Plant Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
authors.forename: Yingfeng
authors.initials: Y
authors.lastname: Wang
authors.forename: Zhibin
authors.initials: Z
authors.lastname: Huang
authors.forename: Yong
authors.initials: Y
authors.lastname: Wu
authors.forename: Russell L
authors.initials: RL
authors.lastname: Malmberg
authors.forename: Liming
authors.initials: L
authors.lastname: Cai
mesh_terms: D016678:Genome; D023281:Genomics / Q000379:methods*; D020407:Internet; D008390:Markov Chains; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012313:RNA