RAG-Web: RNA structure prediction/design using RNA-As-Graphs

Abstract

Abstract Summary We launch a webserver for RNA structure prediction and design corresponding to tools developed using our RNA-As-Graphs (RAG) approach. RAG uses coarse-grained tree graphs to represent RNA secondary structure, allowing the application of graph theory to analyze and advance RNA structure discovery. Our webserver consists of three modules: (a) RAG Sampler: samples tree graph topologies from an RNA secondary structure to predict corresponding tertiary topologies, (b) RAG Builder: builds three-dimensional atomic models from candidate graphs generated by RAG Sampler, and (c) RAG Designer: designs sequences that fold onto novel RNA motifs (described by tree graph topologies). Results analyses are performed for further assessment/selection. The Results page provides links to download results and indicates possible errors encountered. RAG-Web offers a user-friendly interface to utilize our RAG software suite to predict and design RNA structures and sequences. Availability and implementation The webserver is freely available online at: http://www.biomath.nyu.edu/ragtop/. Supplementary information Supplementary data are available at Bioinformatics online.