title: ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors.
abstract: BACKGROUND
  microRNAs (miRNAs) play a vital role in development, oncogenesis, and apoptosis by binding to mRNAs to regulate the posttranscriptional level of coding genes in mammals, plants, and insects. Recent studies have demonstrated that the expression of viral miRNAs is associated with the ability of the virus to infect a host. Identifying potential viral miRNAs from experimental sequence data is valuable for deciphering virus-host interactions. Thus far, a specific predictive model for viral miRNA identification has yet to be developed.
  
  
  RESULTS
  Here, we present ViralmiR for identifying viral miRNA precursors on the basis of sequencing and structural information. We collected 263 experimentally validated miRNA precursors (pre-miRNAs) from 26 virus species and generated sequencing fragments from virus and human genomes as the negative dataset. Support vector machine and random forest models were established using 54 features from RNA sequences and secondary structural information. The results show that ViralmiR achieved a balanced accuracy higher than 83%, which is superior to that of previously developed tools for identifying pre-miRNAs.
  
  
  CONCLUSIONS
  The easy-to-use ViralmiR web interface has been provided as a helpful resource for researchers to use in analyzing and deciphering virus-host interactions. The web interface of ViralmiR can be accessed at http://csb.cse.yzu.edu.tw/viralmir/.
authors.forename: Kai-Yao
authors.initials: KY
authors.lastname: Huang
authors.forename: Tzong-Yi
authors.initials: TY
authors.lastname: Lee
authors.forename: Yu-Chuan
authors.initials: YC
authors.lastname: Teng
authors.forename: Tzu-Hao
authors.initials: TH
authors.lastname: Chang
mesh_terms: D019295:Computational Biology / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D060388:Support Vector Machine
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors; D012333:RNA, Messenger; D012367:RNA, Viral