title: Computational Detection of piRNA in Human Using Support Vector Machine.
abstract: BACKGROUND
  Piwi-interacting RNAs (piRNAs) are small non-coding RNAs (ncRNAs), with a length of about 24-32 nucleotides, which have been discovered recently. These ncRNAs play an important role in germline development, transposon silencing, epigenetic regulation, protecting the genome from invasive transposable elements, and the pathophysiology of diseases such as cancer. piRNA identification is challenging due to the lack of conserved piRNA sequences and structural elements.
  
  
  METHODS
  To detect piRNAs, an appropriate feature set, including 8 diverse feature groups to encode each RNA was applied. In addition, a Support Vector Machine (SVM) classifier was used with optimized parameters for RNA classification. According to the obtained results, the classification performance using the optimized feature subsets was much higher than the one in previously published studies.
  
  
  RESULTS
  Our results revealed 98% accuracy, Mathew' correlation coefficient of 98% and 99% specificity in discriminating piRNAs from the other RNAs. Also, the obtained results show that the proposed method outperforms its competitors.
  
  
  CONCLUSIONS
  In this paper, a prediction method was proposed to identify piRNA in human. Also, 48 heterogeneous features (sequence and structural features) were used to encode RNAs. To assess the performance of the method, a benchmark dataset containing 515 piRNAs and 1206 types of other RNAs was constructed. Our method reached the accuracy of 99% on the benchmark dataset. Also, our analysis revealed that the structural features are the most contributing features in piRNA prediction.
authors: Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
authors: Atefeh
authors: A
authors: Seyeddokht
authors: Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
authors: Ali Asghar
authors: AA
authors: Aslaminejad
authors: Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
authors: Ali
authors: A
authors: Masoudi-Nejad
authors: Department of Animal Science, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
authors: Mohammadreza
authors: M
authors: Nassiri
authors: Bioinformatics and Computational Omics. LAB (BioCOOL), Faculty of Biological Sciences, Tarbiat Modares University (TMU), Tehran, Iran.
authors: Javad
authors: J
authors: Zahiri
authors: Department of Food Hygiene and Public Health, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran.
authors: Balal
authors: B
authors: Sadeghi
keywords: Piwi-interacting RNAs (piRNAs); RNA; Support Vector Machines (SVM)