title: PSoL: a positive sample only learning algorithm for finding non-coding RNA genes.
abstract: BACKGROUND
  Small non-coding RNA (ncRNA) genes play important regulatory roles in a variety of cellular processes. However, detection of ncRNA genes is a great challenge to both experimental and computational approaches. In this study, we describe a new approach called positive sample only learning (PSoL) to predict ncRNA genes in the Escherichia coli genome. Although PSoL is a machine learning method for classification, it requires no negative training data, which, in general, is hard to define properly and affects the performance of machine learning dramatically. In addition, using the support vector machine (SVM) as the core learning algorithm, PSoL can integrate many different kinds of information to improve the accuracy of prediction. Besides the application of PSoL for predicting ncRNAs, PSoL is applicable to many other bioinformatics problems as well.
  
  
  RESULTS
  The PSoL method is assessed by 5-fold cross-validation experiments which show that PSoL can achieve about 80% accuracy in recovery of known ncRNAs. We compared PSoL predictions with five previously published results. The PSoL method has the highest percentage of predictions overlapping with those from other methods.
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720, USA.
authors.forename: Chunlin
authors.initials: C
authors.lastname: Wang
authors.forename: Chris
authors.initials: C
authors.lastname: Ding
authors.forename: Richard F
authors.initials: RF
authors.lastname: Meraz
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Holbrook
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics*; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods; D012329:RNA, Bacterial / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012329:RNA, Bacterial; D022661:RNA, Untranslated