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BEAM web server: a tool for structural RNA motif discovery
MOTIVATION: RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860439/ https://www.ncbi.nlm.nih.gov/pubmed/29095974 http://dx.doi.org/10.1093/bioinformatics/btx704 |
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author | Pietrosanto, Marco Adinolfi, Marta Casula, Riccardo Ausiello, Gabriele Ferrè, Fabrizio Helmer-Citterich, Manuela |
author_facet | Pietrosanto, Marco Adinolfi, Marta Casula, Riccardo Ausiello, Gabriele Ferrè, Fabrizio Helmer-Citterich, Manuela |
author_sort | Pietrosanto, Marco |
collection | PubMed |
description | MOTIVATION: RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. RESULTS: The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. AVAILABILITY AND IMPLEMENTATION: The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-5860439 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-58604392018-03-28 BEAM web server: a tool for structural RNA motif discovery Pietrosanto, Marco Adinolfi, Marta Casula, Riccardo Ausiello, Gabriele Ferrè, Fabrizio Helmer-Citterich, Manuela Bioinformatics Applications Notes MOTIVATION: RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. RESULTS: The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. AVAILABILITY AND IMPLEMENTATION: The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2018-03-15 2017-10-31 /pmc/articles/PMC5860439/ /pubmed/29095974 http://dx.doi.org/10.1093/bioinformatics/btx704 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Applications Notes Pietrosanto, Marco Adinolfi, Marta Casula, Riccardo Ausiello, Gabriele Ferrè, Fabrizio Helmer-Citterich, Manuela BEAM web server: a tool for structural RNA motif discovery |
title | BEAM web server: a tool for structural RNA motif discovery |
title_full | BEAM web server: a tool for structural RNA motif discovery |
title_fullStr | BEAM web server: a tool for structural RNA motif discovery |
title_full_unstemmed | BEAM web server: a tool for structural RNA motif discovery |
title_short | BEAM web server: a tool for structural RNA motif discovery |
title_sort | beam web server: a tool for structural rna motif discovery |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860439/ https://www.ncbi.nlm.nih.gov/pubmed/29095974 http://dx.doi.org/10.1093/bioinformatics/btx704 |
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