title: Prediction of piRNAs using transposon interaction and a support vector machine.
abstract: BACKGROUND
  Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNA primarily expressed in germ cells that can silence transposons at the post-transcriptional level. Accurate prediction of piRNAs remains a significant challenge.
  
  
  RESULTS
  We developed a program for piRNA annotation (Piano) using piRNA-transposon interaction information. We downloaded 13,848 Drosophila piRNAs and 261,500 Drosophila transposons. The piRNAs were aligned to transposons with a maximum of three mismatches. Then, piRNA-transposon interactions were predicted by RNAplex. Triplet elements combining structure and sequence information were extracted from piRNA-transposon matching/pairing duplexes. A support vector machine (SVM) was used on these triplet elements to classify real and pseudo piRNAs, achieving 95.3 ± 0.33% accuracy and 96.0 ± 0.5% sensitivity. The SVM classifier can be used to correctly predict human, mouse and rat piRNAs, with overall accuracy of 90.6%. We used Piano to predict piRNAs for the rice stem borer, Chilo suppressalis, an important rice insect pest that causes huge yield loss. As a result, 82,639 piRNAs were predicted in C. suppressalis.
  
  
  CONCLUSIONS
  Piano demonstrates excellent piRNA prediction performance by using both structure and sequence features of transposon-piRNAs interactions. Piano is freely available to the academic community at http://ento.njau.edu.cn/Piano.html .
authors.affiliation: Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China. wangk4@miamioh.edu.|Currently affiliation: Department of Biology, Miami University, Oxford, OH, 45056, USA. wangk4@miamioh.edu.
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.affiliation: Department of Biology, Miami University, Oxford, OH, 45056, USA. liangc@miamioh.edu.|Department of Computer Science and software Engineering, Miami University, Oxford, OH, 45056, USA. liangc@miamioh.edu.
authors.forename: Chun
authors.initials: C
authors.lastname: Liang
authors.affiliation: Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China. liujd@njau.edu.cn.|College of Information and Technology, Nanjing Agricultural University, Nanjing, 210095, China. liujd@njau.edu.cn.
authors.forename: Jinding
authors.initials: J
authors.lastname: Liu
authors.affiliation: Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China. xiaohuamei625@163.com.
authors.forename: Huamei
authors.initials: H
authors.lastname: Xiao
authors.affiliation: College of Information and Technology, Nanjing Agricultural University, Nanjing, 210095, China. sqhuang@njau.edu.cn.
authors.forename: Shuiqing
authors.initials: S
authors.lastname: Huang
authors.affiliation: College of computer science and Technology, Nanjing Normal University, Nanjing, 210023, China. xujianghua@njnu.edu.cn.
authors.forename: Jianhua
authors.initials: J
authors.lastname: Xu
authors.affiliation: Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China. lifei03@tsinghua.org.cn.
authors.forename: Fei
authors.initials: F
authors.lastname: Li
mesh_terms: D000818:Animals; D029721:Drosophila Proteins / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics; D006801:Humans; D051379:Mice; D009036:Moths / Q000235:genetics* / Q000378:metabolism; D012275:Oryza / Q000469:parasitology*; D034741:RNA, Small Interfering / Q000235:genetics*; D051381:Rats; D060388:Support Vector Machine; D014584:User-Computer Interface
chemical_list: D029721:Drosophila Proteins; D034741:RNA, Small Interfering