SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification.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 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.  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.  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.
snoReport
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. 
RNA secondary structure prediction
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. 
machine learning
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. 
SVM training phase