Título:	SnoReport 2.0 : new features and a refined Support Vector Machine to improve snoRNA identification
Autor(es):	Oliveira, João Victor de Araujo Costa, Fabrizio Backofen, Rolf Stadler, Peter Florian Walter, Maria Emília Machado Telles Hertel, Jana
Assunto:	Ácido ribonucléico Biologia computacional Aprendizado do computador
Data de publicação:	15-Dez-2016
Editora:	BioMedCentral
Referência:	OLIVEIRA, João Victor de Araújo de et al. SnoReport 2.0: new features and a refined support vector machine to improve snoRNA identification. BMC Bioinformatics, v. 17, supl. 18, 2016. Disponível em: <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1345-6>. Acesso em: 25 jun. 2018. doi: https://doi.org/10.1186/s12859-016-1345-6.
Abstract:	Background: snoReport uses RNA secondary structure prediction combined with machine learning as the basis to identify the two main classes of small nucleolar RNAs, the box H/ACA snoRNAs and the box C/D snoRNAs. Here, we present snoReport 2.0, which substantially improves and extends in the original method by: extracting new features for both box C/D and H/ACA box snoRNAs; developing a more sophisticated technique in the SVM training phase with recent data from vertebrate organisms and a careful choice of the SVM parameters C and γ ; and using updated versions of tools and databases used for the construction of the original version of snoReport. To validate the new version and to demonstrate its improved performance, we tested snoReport 2.0 in different organisms. Results: Results of the training and test phases of boxes H/ACA and C/D snoRNAs, in both versions of snoReport, are discussed. Validation on real data was performed to evaluate the predictions of snoReport 2.0. Our program was applied to a set of previously annotated sequences, some of them experimentally confirmed, of humans, nematodes, drosophilids, platypus, chickens and leishmania. We significantly improved the predictions for vertebrates, since the training phase used information of these organisms, but H/ACA box snoRNAs identification was improved for the other ones. Conclusion: We presented snoReport 2.0, to predict H/ACA box and C/D box snoRNAs, an efficient method to find true positives and avoid false positives in vertebrate organisms. H/ACA box snoRNA classifier showed an F-score of 93 % (an improvement of 10 % regarding the previous version), while C/D box snoRNA classifier, an F-Score of 94 % (improvement of 14 %). Besides, both classifiers exhibited performance measures above 90 %. These results show that snoReport 2.0 avoid false positives and false negatives, allowing to predict snoRNAs with high quality. In the validation phase, snoReport 2.0 predicted 67.43 % of vertebrate organisms for both classes. For Nematodes and Drosophilids, 69 % and 76.67 %, for H/ACA box snoRNAs were predicted, respectively, showing that snoReport 2.0 is good to identify snoRNAs in vertebrates and also H/ACA box snoRNAs in invertebrates organisms.
Licença:	© The Author(s). 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
DOI:	https://doi.org/10.1186/s12859-016-1345-6
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