title: The prediction of the porcine pre-microRNAs in genome-wide based on support vector machine (SVM) and homology searching.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate gene expression by targeting mRNAs for translation repression or mRNA degradation. Although many miRNAs have been discovered and studied in human and mouse, few studies focused on porcine miRNAs, especially in genome wide.
  
  
  RESULTS
  Here, we adopted computational approaches including support vector machine (SVM) and homology searching to make a global scanning on the pre-miRNAs of pigs. In our study, we built the SVM-based porcine pre-miRNAs classifier with a sensitivity of 100%, a specificity of 91.2% and a total prediction accuracy of 95.6%, respectively. Moreover, 2204 novel porcine pre-miRNA candidates were found by using SVM-based pre-miRNAs classifier. Besides, 116 porcine pre-miRNA candidates were detected by homology searching.
  
  
  CONCLUSIONS
  We identified the porcine pre-miRNA in genome-wide through computational approaches by utilizing the data sets of pigs and set up the porcine pre-miRNAs library which may provide us a global scanning on the pre-miRNAs of pigs in genome level and would benefit subsequent experimental research on porcine miRNA functional and expression analysis.
authors.affiliation: School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Wang
authors.forename: Kan
authors.initials: K
authors.lastname: He
authors.forename: Qishan
authors.initials: Q
authors.lastname: Wang
authors.forename: Yumei
authors.initials: Y
authors.lastname: Yang
authors.forename: Yuchun
authors.initials: Y
authors.lastname: Pan
mesh_terms: D000818:Animals; D020029:Base Pairing / Q000235:genetics; D019295:Computational Biology; D015723:Gene Library; D005822:Genetic Vectors / Q000235:genetics; D016678:Genome / Q000235:genetics*; D035683:MicroRNAs / Q000145:classification / Q000235:genetics*; D008957:Models, Genetic; D011237:Predictive Value of Tests; D012680:Sensitivity and Specificity; D017385:Sequence Homology; D013552:Swine / Q000235:genetics*
chemical_list: D035683:MicroRNAs