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Bioinformatics. 2013 Nov 15;29(22):2928-30. doi: 10.1093/bioinformatics/btt495. Epub 2013 Aug 23.

catRAPID omics: a web server for large-scale prediction of protein-RNA interactions.

Author information

1
Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.

Abstract

SUMMARY:

Here we introduce catRAPID omics, a server for large-scale calculations of protein-RNA interactions. Our web server allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences without size restriction; (iii) analysis of nucleic acid binding regions in proteins; and (iv) detection of RNA motifs involved in protein recognition.

RESULTS:

We developed a web server to allow fast calculation of ribonucleoprotein associations in Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae and Xenopus tropicalis (custom libraries can be also generated). The catRAPID omics was benchmarked on the recently published RNA interactomes of Serine/arginine-rich splicing factor 1 (SRSF1), Histone-lysine N-methyltransferase EZH2 (EZH2), TAR DNA-binding protein 43 (TDP43) and RNA-binding protein FUS (FUS) as well as on the protein interactomes of U1/U2 small nucleolar RNAs, X inactive specific transcript (Xist) repeat A region (RepA) and Crumbs homolog 3 (CRB3) 3'-untranslated region RNAs. Our predictions are highly significant (P < 0.05) and will help the experimentalist to identify candidates for further validation.

AVAILABILITY:

catRAPID omics can be freely accessed on the Web at http://s.tartaglialab.com/catrapid/omics. Documentation, tutorial and FAQs are available at http://s.tartaglialab.com/page/catrapid_group.

PMID:
23975767
PMCID:
PMC3810848
DOI:
10.1093/bioinformatics/btt495
[Indexed for MEDLINE]
Free PMC Article

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