title: MatPred: Computational Identification of Mature MicroRNAs within Novel Pre-MicroRNAs.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are short noncoding RNAs integral for regulating gene expression at the posttranscriptional level. However, experimental methods often fall short in finding miRNAs expressed at low levels or in specific tissues. While several computational methods have been developed for predicting the localization of mature miRNAs within the precursor transcript, the prediction accuracy requires significant improvement.
  
  
  RESULTS
  Here, we present MatPred, which predicts mature miRNA candidates within novel pre-miRNA transcripts. In addition to the relative locus of the mature miRNA within the pre-miRNA hairpin loop and minimum free energy, we innovatively integrated features that describe the nucleotide-specific RNA secondary structure characteristics. In total, 94 features were extracted from the mature miRNA loci and flanking regions. The model was trained based on a radial basis function kernel/support vector machine (RBF/SVM). Our method can predict precise locations of mature miRNAs, as affirmed by experimentally verified human pre-miRNAs or pre-miRNAs candidates, thus achieving a significant advantage over existing methods.
  
  
  CONCLUSIONS
  MatPred is a highly effective method for identifying mature miRNAs within novel pre-miRNA transcripts. Our model significantly outperformed three other widely used existing methods. Such processing prediction methods may provide important insight into miRNA biogenesis.
authors.affiliation: Institute of Biomedical Engineering, College of Automation, Harbin Engineering University, 145 Nantong Street, Nangang District, Harbin, Heilongjiang 150001, China ; Bioinformatics Research Center, College of Automation, Harbin Engineering University, 145 Nantong Street, Nangang District, Harbin, Heilongjiang 150001, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Li
authors.affiliation: Institute of Biomedical Engineering, College of Automation, Harbin Engineering University, 145 Nantong Street, Nangang District, Harbin, Heilongjiang 150001, China ; Network Information Center, Qiqihar University, No. 42, Wenhua Street, Qiqihar, Heilongjiang 161006, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Institute of Biomedical Engineering, College of Automation, Harbin Engineering University, 145 Nantong Street, Nangang District, Harbin, Heilongjiang 150001, China ; Bioinformatics Research Center, College of Automation, Harbin Engineering University, 145 Nantong Street, Nangang District, Harbin, Heilongjiang 150001, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.affiliation: Bioinformatics Research Center, College of Automation, Harbin Engineering University, 145 Nantong Street, Nangang District, Harbin, Heilongjiang 150001, China.
authors.forename: Weixing
authors.initials: W
authors.lastname: Feng
authors.affiliation: Institute of Biomedical Engineering, College of Automation, Harbin Engineering University, 145 Nantong Street, Nangang District, Harbin, Heilongjiang 150001, China.
authors.forename: Kuan
authors.initials: K
authors.lastname: Luan
authors.affiliation: Network Information Center, Qiqihar University, No. 42, Wenhua Street, Qiqihar, Heilongjiang 161006, China.
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Dai
authors.affiliation: Institute of Biomedical Engineering, College of Automation, Harbin Engineering University, 145 Nantong Street, Nangang District, Harbin, Heilongjiang 150001, China.
authors.forename: Chengzhen
authors.initials: C
authors.lastname: Xu
authors.affiliation: Institute of Biomedical Engineering, College of Automation, Harbin Engineering University, 145 Nantong Street, Nangang District, Harbin, Heilongjiang 150001, China.
authors.forename: Xianglian
authors.initials: X
authors.lastname: Meng
authors.affiliation: Institute of Biomedical Engineering, College of Automation, Harbin Engineering University, 145 Nantong Street, Nangang District, Harbin, Heilongjiang 150001, China.
authors.forename: Qiushi
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Institute of Biomedical Engineering, College of Automation, Harbin Engineering University, 145 Nantong Street, Nangang District, Harbin, Heilongjiang 150001, China ; Bioinformatics Research Center, College of Automation, Harbin Engineering University, 145 Nantong Street, Nangang District, Harbin, Heilongjiang 150001, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Liang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D012322:RNA Precursors / Q000235:genetics*; D060388:Support Vector Machine
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors