Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Pietrosanto, Marco, Adinolfi, Marta, Casula, Riccardo, Ausiello, Gabriele, Ferrè, Fabrizio, Helmer-Citterich, Manuela
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
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
_version_ 1783307974108774400
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
work_keys_str_mv AT pietrosantomarco beamwebserveratoolforstructuralrnamotifdiscovery
AT adinolfimarta beamwebserveratoolforstructuralrnamotifdiscovery
AT casulariccardo beamwebserveratoolforstructuralrnamotifdiscovery
AT ausiellogabriele beamwebserveratoolforstructuralrnamotifdiscovery
AT ferrefabrizio beamwebserveratoolforstructuralrnamotifdiscovery
AT helmercitterichmanuela beamwebserveratoolforstructuralrnamotifdiscovery