title: Predicting human microRNA precursors based on an optimized feature subset generated by GA-SVM.
abstract: MicroRNAs (miRNAs) are non-coding RNAs that play important roles in post-transcriptional regulation. Identification of miRNAs is crucial to understanding their biological mechanism. Recently, machine-learning approaches have been employed to predict miRNA precursors (pre-miRNAs). However, features used are divergent and consequently induce different performance. Thus, feature selection is critical for pre-miRNA prediction. We generated an optimized feature subset including 13 features using a hybrid of genetic algorithm and support vector machine (GA-SVM). Based on SVM, the classification performance of the optimized feature subset is much higher than that of the two feature sets used in microPred and miPred by five-fold cross-validation. Finally, we constructed the classifier miR-SF to predict the most recently identified human pre-miRNAs in miRBase (version 16). Compared with microPred and miPred, miR-SF achieved much higher classification performance. Accuracies were 93.97%, 86.21% and 64.66% for miR-SF, microPred and miPred, respectively. Thus, miR-SF is effective for identifying pre-miRNAs.
authors.affiliation: College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China.
authors.forename: Yanqiu
authors.initials: Y
authors.lastname: Wang
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Chen
authors.forename: Wei
authors.initials: W
authors.lastname: Jiang
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Lei
authors.initials: L
authors.lastname: Yang
authors.forename: Mingzhi
authors.initials: M
authors.lastname: Liao
authors.forename: Baofeng
authors.initials: B
authors.lastname: Lian
authors.forename: Yingli
authors.initials: Y
authors.lastname: Lv
authors.forename: Shiyuan
authors.initials: S
authors.lastname: Wang
authors.forename: Shuyuan
authors.initials: S
authors.lastname: Wang
authors.forename: Xia
authors.initials: X
authors.lastname: Li
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001483:Base Sequence; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors; D034741:RNA, Small Interfering