Títol:
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omiXcore: a web server for prediction of protein interactions with large RNA
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Autor/a:
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Armaos, Alexandros; Cirillo, Davide; Tartaglia, Gian Gaetano
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Abstract:
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SUMMARY: Here we introduce omiXcore, a server for calculations of protein binding to large RNAs (> 500 nucleotides). Our webserver allows (i) use of both protein and RNA sequences without size restriction, (ii) pre-compiled library for exploration of human long intergenic RNAs interactions and (iii) prediction of binding sites. RESULTS: omiXcore was trained and tested on enhanced UV Cross-Linking and ImmunoPrecipitation data. The method discriminates interacting and non-interacting protein-RNA pairs and identifies RNA binding sites with Areas under the ROC curve > 0.80, which suggests that the tool is particularly useful to prioritize candidates for further experimental validation.
AVAILABILITY AND IMPLEMENTATION: omiXcore is freely accessed on the web at http://service.tartaglialab.com/grant_submission/omixcore. CONTACT: gian.tartaglia@crg.es. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
Abstract:
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We acknowledge support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’ and the CERCA Programme / Generalitat de Catalunya. This work was supported by the European Union Seventh Framework Programme [FP7/2007-13], European Research Council RIBOMYLOME_309545 (Gian Gaetano Tartaglia) and Spanish Ministry of Economy and Competitiveness BFU2014-5505-P (Gian Gaetano Tartaglia) |
Matèries:
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-Interaccions RNA-proteïna -Programes d'ordinador |
Drets:
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© Alexandros Armaos, Davide Cirillo, Gian Gaetano Tartaglia 2017. Published by Oxford University Press. This is an Open Access article distributed under the terms of a Creative Commons Attribution License
http://creativecommons.org/licenses/by-nc/4.0/ |
Tipus de document:
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Article Article - Versió publicada |
Publicat per:
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Oxford University Press
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