Summary: Here we introduce catRAPID omics, a server for largescale 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 RNAbinding 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. © The Author 2013. Published by Oxford University Press. All rights reserved.

CatRAPID omics: A web server for large-scale prediction of protein-RNA interactions / Agostini, Federico; Zanzoni, Andreas; Klus, Petr; Marchese, Domenica; Cirillo, Davide; Tartaglia, Gian Gaetano. - In: BIOINFORMATICS. - ISSN 1367-4803. - 29:22(2013), pp. 2928-2930. [10.1093/bioinformatics/btt495]

CatRAPID omics: A web server for large-scale prediction of protein-RNA interactions

Marchese, Domenica;Tartaglia, Gian Gaetano
2013

Abstract

Summary: Here we introduce catRAPID omics, a server for largescale 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 RNAbinding 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. © The Author 2013. Published by Oxford University Press. All rights reserved.
2013
3' Untranslated Regions; algorithms; animals; caenorhabditis elegans; gene expression profiling; humans; Internet; mice; nucleotide motifs; protein structure, tertiary; proteomics; RNA; RNA-binding proteins; Rats; sequence analysis, Protein; Sequence Analysis, RNA; Software; Statistics and Probability; Biochemistry; Molecular Biology; Computer Science Applications1707 Computer Vision and Pattern Recognition; Computational Theory and Mathematics; Computational Mathematics
01 Pubblicazione su rivista::01a Articolo in rivista
CatRAPID omics: A web server for large-scale prediction of protein-RNA interactions / Agostini, Federico; Zanzoni, Andreas; Klus, Petr; Marchese, Domenica; Cirillo, Davide; Tartaglia, Gian Gaetano. - In: BIOINFORMATICS. - ISSN 1367-4803. - 29:22(2013), pp. 2928-2930. [10.1093/bioinformatics/btt495]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/1279525
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