ATtRACT—a database of RNA-binding proteins and associated motifs
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 a...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823821/ https://www.ncbi.nlm.nih.gov/pubmed/27055826 http://dx.doi.org/10.1093/database/baw035 |
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author | Giudice, Girolamo Sánchez-Cabo, Fátima Torroja, Carlos Lara-Pezzi, Enrique |
author_facet | Giudice, Girolamo Sánchez-Cabo, Fátima Torroja, Carlos Lara-Pezzi, Enrique |
author_sort | Giudice, Girolamo |
collection | PubMed |
description | 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. Database URL: http:// attract. cnic. es |
format | Online Article Text |
id | pubmed-4823821 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-48238212016-04-08 ATtRACT—a database of RNA-binding proteins and associated motifs Giudice, Girolamo Sánchez-Cabo, Fátima Torroja, Carlos Lara-Pezzi, Enrique Database (Oxford) Original Article 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. Database URL: http:// attract. cnic. es Oxford University Press 2016-04-06 /pmc/articles/PMC4823821/ /pubmed/27055826 http://dx.doi.org/10.1093/database/baw035 Text en © The Author(s) 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Article Giudice, Girolamo Sánchez-Cabo, Fátima Torroja, Carlos Lara-Pezzi, Enrique ATtRACT—a database of RNA-binding proteins and associated motifs |
title | ATtRACT—a database of RNA-binding proteins and associated motifs |
title_full | ATtRACT—a database of RNA-binding proteins and associated motifs |
title_fullStr | ATtRACT—a database of RNA-binding proteins and associated motifs |
title_full_unstemmed | ATtRACT—a database of RNA-binding proteins and associated motifs |
title_short | ATtRACT—a database of RNA-binding proteins and associated motifs |
title_sort | attract—a database of rna-binding proteins and associated motifs |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823821/ https://www.ncbi.nlm.nih.gov/pubmed/27055826 http://dx.doi.org/10.1093/database/baw035 |
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