title: Riboswitch finder--a tool for identification of riboswitch RNAs.
abstract: We describe a dedicated RNA motif search program and web server to identify RNA riboswitches. The Riboswitch finder analyses a given sequence using the web interface, checks specific sequence elements and secondary structure, calculates and displays the energy folding of the RNA structure and runs a number of tests including this information to determine whether high-sensitivity riboswitch motifs (or variants) according to the Bacillus subtilis type are present in the given RNA sequence. Batch-mode determination (all sequences input at once and separated by FASTA format) is also possible. The program has been implemented and is available both as local software for in-house installation and as a web server at http://www.biozentrum.uni-wuerzburg.de/bioinformatik/Riboswitch/.
authors.affiliation: Biochemiezentrum, Project Group B2 (Dandekar/Schirmer), University of Heidelberg, Im Neuenheimer Feld 504, 69120 Heidelberg, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Bengert
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
mesh_terms: D000494:Allosteric Regulation; D020407:Internet; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D038621:Regulatory Sequences, Ribonucleic Acid; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012333:RNA, Messenger; D038621:Regulatory Sequences, Ribonucleic Acid