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CROSSalive: a web server for predicting the in vivo structure of RNA molecules

Riccardo Delli Ponti, Alexandros Armaos, View ORCID ProfileGian Gaetano Tartaglia
doi: https://doi.org/10.1101/626085
Riccardo Delli Ponti
1Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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Alexandros Armaos
1Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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Gian Gaetano Tartaglia
1Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
3Institucio Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluıs Companys, 08010 Barcelona, Spain
4Department of Biology ‘Charles Darwin’, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
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  • ORCID record for Gian Gaetano Tartaglia
  • For correspondence: gian@tartaglialab.com
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ABSTRACT

Here we introduce CROSSalive, an algorithm to predict the RNA secondary structure profile (double and single stranded regions) in vivo and without sequence length limitations. Using predictions of protein interactions CROSSalive predicts the effect of N6 adenosine methylation (m6a) on RNA structure. Trained on icSHAPE data in presence (m6a+) and absence (m6a-) of methylation CROSSalive achieves an accuracy of 0.88 on the test set. The algorithm was also applied to the murine long non-coding RNA Xist (17900 nt, not present in the training) and shows a Pearson’s correlation of 0.45 with SHAPE-map data. CROSSalive webserver is freely accessible at the following page: http://service.tartaglialab.com/new_submission/crossalive

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  • http://service.tartaglialab.com/new_submission/crossalive

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 11, 2019.
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CROSSalive: a web server for predicting the in vivo structure of RNA molecules
Riccardo Delli Ponti, Alexandros Armaos, Gian Gaetano Tartaglia
bioRxiv 626085; doi: https://doi.org/10.1101/626085
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CROSSalive: a web server for predicting the in vivo structure of RNA molecules
Riccardo Delli Ponti, Alexandros Armaos, Gian Gaetano Tartaglia
bioRxiv 626085; doi: https://doi.org/10.1101/626085

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