title: The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures.
abstract: Many non-coding RNA genes and cis-acting regulatory elements of mRNAs contain RNA secondary structures that are critical for their function. Such functional RNAs can be predicted on the basis of thermodynamic stability and evolutionary conservation. We present a web server that uses the RNAz algorithm to detect functional RNA structures in multiple alignments of nucleotide sequences. The server provides access to a complete and fully automatic analysis pipeline that allows not only to analyze single alignments in a variety of formats, but also to conduct complex screens of large genomic regions. Results are presented on a website that is illustrated by various structure representations and can be downloaded for local view. The web server is available at: rna.tbi.univie.ac.at/RNAz.
authors: Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria.
authors: Andreas R
authors: AR
authors: Gruber
authors: Richard
authors: R
authors: Neuböck
authors: Ivo L
authors: IL
authors: Hofacker
authors: Stefan
authors: S
authors: Washietl
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D019143:Evolution, Molecular; D016678:Genome; D020407:Internet; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D038621:Regulatory Sequences, Ribonucleic Acid; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D013816:Thermodynamics
chemical_list: D038621:Regulatory Sequences, Ribonucleic Acid; D012313:RNA