catRAPID signature: identification of ribonucleoproteins and RNA-binding regions

Livi, Carmen Maria; Klus, Petr, 1985-; Delli Ponti, Riccardo, 1987-; Tartaglia, Gian Gaetano

doi:http://dx.doi.org/10.1093/bioinformatics/btv629

catRAPID signature: identification of ribonucleoproteins and RNA-binding regions

License

Citation

Livi CM, Klus P, Delli Ponti R, Tartaglia GG. catRAPID signature: identification of ribonucleoproteins and RNA-binding regions. Bioinformatics. 2016;32(5):773-5. DOI 10.1093/bioinformatics/btv629

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