پژوهش های تولیدات دامی, Volume (8), No (1), Year (2016-1) , Pages (36-41)

Title : ( Computational Detection of piRNA in Human Using Support Vector Machine )

Authors: Atefeh Seyeddokht Dehbar , Ali Asghar Aslaminejad , Ali Masoudi-Nejad , Mohammadreza Nassiri , Javad Zahiri , Balal Sadeghi ,

Citation: BibTeX | EndNote

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 germlinedevelopment, 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 piRNAsfrom the other RNAs. Also, the obtained results show that the proposed method outperforms its competitors. Conclusion: 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.

Keywords

, Piwi-interacting RNAs (piRNAs), RNA, Support Vector Machines (SVM)
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@article{paperid:1056728,
author = {Seyeddokht Dehbar, Atefeh and Aslaminejad, Ali Asghar and Ali Masoudi-Nejad and Nassiri, Mohammadreza and Javad Zahiri and Balal Sadeghi},
title = {Computational Detection of piRNA in Human Using Support Vector Machine},
journal = {پژوهش های تولیدات دامی},
year = {2016},
volume = {8},
number = {1},
month = {January},
issn = {۲۲۵۱-۸۶۲۲},
pages = {36--41},
numpages = {5},
keywords = {Piwi-interacting RNAs (piRNAs); RNA; Support Vector Machines (SVM)},
}

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%0 Journal Article
%T Computational Detection of piRNA in Human Using Support Vector Machine
%A Seyeddokht Dehbar, Atefeh
%A Aslaminejad, Ali Asghar
%A Ali Masoudi-Nejad
%A Nassiri, Mohammadreza
%A Javad Zahiri
%A Balal Sadeghi
%J پژوهش های تولیدات دامی
%@ ۲۲۵۱-۸۶۲۲
%D 2016

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