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dc.contributor.author | Giudice, Girolamo | |
dc.contributor.author | Sanchez-Cabo, Fatima | |
dc.contributor.author | Torroja, Carlos | |
dc.contributor.author | Lara-Pezzi, Enrique | |
dc.date.accessioned | 2017-10-30T13:32:25Z | |
dc.date.available | 2017-10-30T13:32:25Z | |
dc.date.issued | 2016 | |
dc.identifier | ISI:000374095000001 | |
dc.identifier.citation | Database (Oxford). 2016; 2016:baw035 | |
dc.identifier.issn | 1758-0463 | |
dc.identifier.uri | http://hdl.handle.net/20.500.12105/5239 | |
dc.description.abstract | RNA-binding proteins (RBPs) play a crucial role in key cellular processes, including RNA transport, splicing, polyadenylation and stability. Understanding the interaction between RBPs and RNA is key to improve our knowledge of RNA processing, localization and regulation in a global manner. Despite advances in recent years, a unified non-redundant resource that includes information on experimentally validated motifs, RBPs and integrated tools to exploit this information is lacking. Here, we developed a database named ATtRACT (available at http://attract.cnic.es) that compiles information on 370 RBPs and 1583 RBP consensus binding motifs, 192 of which are not present in any other database. To populate ATtRACT we (i) extracted and hand-curated experimentally validated data from CISBP-RNA, SpliceAid-F, RBPDB databases, (ii) integrated and updated the unavailable ASD database and (iii) extracted information from Protein-RNA complexes present in Protein Data Bank database through computational analyses. ATtRACT provides also efficient algorithms to search a specific motif and scan one or more RNA sequences at a time. It also allows discovering de novo motifs enriched in a set of related sequences and compare them with the motifs included in the database. | |
dc.description.sponsorship | This work was supported by grants from the European Union's Seventh Framework Programme (CardioNext ITN-608027, CardioNeT ITN-289600), from the Spanish Ministry of Science and Innovation (SAF2012-31451) and from the Regional Government of Madrid (2010-BMD-2321 `Fibroteam') to E.L.-P.). Funding for open access charge: EU FP7, grant CardioNext ITN-608027. | |
dc.language.iso | eng | |
dc.publisher | Oxford University Press | |
dc.type.hasVersion | VoR | |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | * |
dc.subject | GENE-REGULATION | |
dc.subject | NUCLEIC-ACID | |
dc.subject | WEB SERVER | |
dc.subject | DISCOVERY | |
dc.subject | SEQUENCES | |
dc.subject | PROGRAM | |
dc.title | ATtRACT-a database of RNA-binding proteins and associated motifs | |
dc.type | journal article | |
dc.rights.license | Atribución 4.0 Internacional | * |
dc.identifier.pubmedID | 27055826 | |
dc.identifier.doi | 10.1093/database/baw035 | |
dc.contributor.funder | European Commission | |
dc.contributor.funder | Ministerio de Economía y Competitividad (España) | |
dc.contributor.funder | Comunidad de Madrid (España) | |
dc.description.peerreviewed | Sí | |
dc.relation.publisherversion | https://doi.org/10.1093/database/baw035 | |
dc.identifier.journal | Database-The Journal of Biological Database and Curation | |
dc.repisalud.orgCNIC | CNIC::Grupos de investigación::Regulación Molecular de la Insuficiencia Cardiaca | |
dc.repisalud.orgCNIC | CNIC::Unidades técnicas::Bioinformática | |
dc.repisalud.institucion | CNIC | |
dc.relation.projectID | info:eu-repo/grantAgreement/EC/FP7/289600 | es_ES |
dc.relation.projectID | info:eu-repo/grantAgreement/EC/FP7/608027 | es_ES |
dc.rights.accessRights | open access | es_ES |