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Bioinformatics. 2016 Mar 1;32(5):773-5. doi: 10.1093/bioinformatics/btv629. Epub 2015 Oct 31.

catRAPID signature: identification of ribonucleoproteins and RNA-binding regions.

Author information

1
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and.
2
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.

Abstract

MOTIVATION:

Recent technological advances revealed that an unexpected large number of proteins interact with transcripts even if the RNA-binding domains are not annotated. We introduce catRAPID signature to identify ribonucleoproteins based on physico-chemical features instead of sequence similarity searches. The algorithm, trained on human proteins and tested on model organisms, calculates the overall RNA-binding propensity followed by the prediction of RNA-binding regions. catRAPID signature outperforms other algorithms in the identification of RNA-binding proteins and detection of non-classical RNA-binding regions. Results are visualized on a webpage and can be downloaded or forwarded to catRAPID omics for predictions of RNA targets.

AVAILABILITY AND IMPLEMENTATION:

catRAPID signature can be accessed at http://s.tartaglialab.com/new_submission/signature

CONTACT:

gian.tartaglia@crg.es or gian@tartaglialab.com

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26520853
PMCID:
PMC4795616
DOI:
10.1093/bioinformatics/btv629
[Indexed for MEDLINE]
Free PMC Article

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