BRIO: a web server for RNA sequence and structure motif scan
| Autor: | Gabriele Ausiello, Marco Pietrosanto, Ilio Vitale, Andrea Guarracino, Francesco Ballesio, Elisa Sangiovanni, Marta Adinolfi, Gerardo Pepe, Manuela Helmer-Citterich |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
RNA Stability
Sequence analysis AcademicSubjects/SCI00010 0206 medical engineering Protein domain RNA-binding protein 02 engineering and technology Computational biology Biology Cell Line 03 medical and health sciences Mice RNA Small Nuclear Genetics Animals Humans Nucleotide Motifs Protein secondary structure 030304 developmental biology Regulation of gene expression 0303 health sciences Internet Base Sequence Sequence Analysis RNA Settore BIO/11 RNA RNA-Binding Proteins Web Server Issue RNA Viral Sequence motif 020602 bioinformatics Software |
| Zdroj: | Nucleic Acids Research |
| Popis: | The interaction between RNA and RNA-binding proteins (RBPs) has a key role in the regulation of gene expression, in RNA stability, and in many other biological processes. RBPs accomplish these functions by binding target RNA molecules through specific sequence and structure motifs. The identification of these binding motifs is therefore fundamental to improve our knowledge of the cellular processes and how they are regulated. Here, we present BRIO (BEAM RNA Interaction mOtifs), a new web server designed for the identification of sequence and structure RNA-binding motifs in one or more RNA molecules of interest. BRIO enables the user to scan over 2508 sequence motifs and 2296 secondary structure motifs identified in Homo sapiens and Mus musculus, in three different types of experiments (PAR-CLIP, eCLIP, HITS). The motifs are associated with the binding of 186 RBPs and 69 protein domains. The web server is freely available at http://brio.bio.uniroma2.it. Graphical Abstract Graphical AbstractInput RNA molecules are folded, encoded using the BEAR alphabet, and scanned for sequence and structure protein binding motifs. Next, for each motif, a statistical test is applied to determine if the motif is enriched in the input RNA molecules with respect to a set of background RNAs. Finally, the collection of the enriched motifs, and their associated proteins, is returned as output. |
| Databáze: | OpenAIRE |
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