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- Title
Accurate Prediction of Transposon-Derived piRNAs by Integrating Various Sequential and Physicochemical Features.
- Authors
Luo, Longqiang; Li, Dingfang; Zhang, Wen; Tu, Shikui; Zhu, Xiaopeng; Tian, Gang
- Abstract
Background: Piwi-interacting RNA (piRNA) is the largest class of small non-coding RNA molecules. The transposon-derived piRNA prediction can enrich the research contents of small ncRNAs as well as help to further understand generation mechanism of gamete. Methods: In this paper, we attempt to differentiate transposon-derived piRNAs from non-piRNAs based on their sequential and physicochemical features by using machine learning methods. We explore six sequence-derived features, i.e. spectrum profile, mismatch profile, subsequence profile, position-specific scoring matrix, pseudo dinucleotide composition and local structure-sequence triplet elements, and systematically evaluate their performances for transposon-derived piRNA prediction. Finally, we consider two approaches: direct combination and ensemble learning to integrate useful features and achieve high-accuracy prediction models. Results: We construct three datasets, covering three species: Human, Mouse and Drosophila, and evaluate the performances of prediction models by 10-fold cross validation. In the computational experiments, direct combination models achieve AUC of 0.917, 0.922 and 0.992 on Human, Mouse and Drosophila, respectively; ensemble learning models achieve AUC of 0.922, 0.926 and 0.994 on the three datasets. Conclusions: Compared with other state-of-the-art methods, our methods can lead to better performances. In conclusion, the proposed methods are promising for the transposon-derived piRNA prediction. The source codes and datasets are available in .
- Subjects
TRANSPOSONS; PIWI genes; NON-coding RNA; PREDICTION theory; MACHINE learning
- Publication
PLoS ONE, 2016, Vol 11, Issue 4, p1
- ISSN
1932-6203
- Publication type
Article
- DOI
10.1371/journal.pone.0153268