RAG-Web: RNA structure prediction/design using RNA-As-Graphs
| Autor: | Tamar Schlick, Grace Meng, Swati Jain, Marva Tariq, Shereef Elmetwaly |
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| Rok vydání: | 2019 |
| Předmět: |
Statistics and Probability
Web server Theoretical computer science Computer science computer.software_genre Network topology Biochemistry Nucleic acid secondary structure 03 medical and health sciences 0302 clinical medicine Nucleic acid structure Molecular Biology 030304 developmental biology 0303 health sciences Software suite RNA Graph theory Tree (graph theory) Applications Notes Graph Computer Science Applications Computational Mathematics Computational Theory and Mathematics Rna structure prediction Nucleic Acid Conformation Databases Nucleic Acid computer 030217 neurology & neurosurgery Algorithms Software MathematicsofComputing_DISCRETEMATHEMATICS |
| Zdroj: | Bioinformatics |
| ISSN: | 1367-4811 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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