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...

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Autores principales: Giudice, Girolamo, Sánchez-Cabo, Fátima, Torroja, Carlos, Lara-Pezzi, Enrique
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
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
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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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