[Show abstract][Hide abstract] ABSTRACT: The Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. It provides
a web interface to the most commonly used programs of the Vienna RNA package. Among them, we find folding of single and aligned
sequences, prediction of RNA–RNA interactions, and design of sequences with a given structure. Additionally, we provide analysis
of folding landscapes using the barriers program and structural RNA alignments using LocARNA. The web server together with
software packages for download is freely accessible at http://rna.tbi.univie.ac.at/.
Full-text · Article · Aug 2008 · Nucleic Acids Research
[Show abstract][Hide abstract] 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.
Full-text · Article · Aug 2007 · Nucleic Acids Research