RBPDB: a database of RNA-binding specificities

TLDR

The RNA‑Binding Protein DataBase (RBPDB) compiles experimentally derived RNA‑binding sites from both in vitro and in vivo studies, curated from primary literature. RBPDB was constructed by surveying literature for binding data on all RNA‑binding proteins with known RNA‑binding domains in human, mouse, fly, and worm, and is accessed via a web interface that supports browsing, searching, exporting, bulk downloads, and sequence scanning for binding sites. The database contains binding data for 272 RBPs, including 71 with position‑weight‑matrix motifs and 36 sets of in vivo‑bound transcript sequences from immunoprecipitation experiments. RBPDB is freely available without registration at http://rbpdb.ccbr.utoronto.ca/.

Abstract

The RNA-Binding Protein DataBase (RBPDB) is a collection of experimental observations of RNA-binding sites, both in vitro and in vivo , manually curated from primary literature. To build RBPDB, we performed a literature search for experimental binding data for all RNA-binding proteins (RBPs) with known RNA-binding domains in four metazoan species (human, mouse, fly and worm). In total, RPBDB contains binding data on 272 RBPs, including 71 that have motifs in position weight matrix format, and 36 sets of sequences of in vivo -bound transcripts from immunoprecipitation experiments. The database is accessible by a web interface which allows browsing by domain or by organism, searching and export of records, and bulk data downloads. Users can also use RBPDB to scan sequences for RBP-binding sites. RBPDB is freely available, without registration at http://rbpdb.ccbr.utoronto.ca/.