Recombination Hotspot/Coldspot Identification Combining Three Different Pseudocomponents via an Ensemble Learning Approach. (25th August 2016)

• Record Type: Journal Article
• Authors: Liu, Bingquan; Liu, Yumeng; Huang, Dong
• Other Names: Ma Qin Academic Editor.
• Is Part Of: BioMed research international. Volume 2016(2016)
• Publication Date: 2016-08-25
• Subjects: Medicine -- Periodicals; Biology -- Periodicals; Biotechnology -- Periodicals; Life sciences -- Periodicals; 610.5
• DOI: 10.1155/2016/8527435
• Languages: English
• ISSNs: 2314-6133

Abstract

Abstract : Recombination presents a nonuniform distribution across the genome. Genomic regions that present relatively higher frequencies of recombination are called hotspots while those with relatively lower frequencies of recombination are recombination coldspots. Therefore, the identification of hotspots/coldspots could provide useful information for the study of the mechanism of recombination. In this study, a new computational predictor called SVM-EL was proposed to identify hotspots/coldspots across the yeast genome. It combined Support Vector Machines (SVMs) and Ensemble Learning (EL) based on three features including basic kmer (Kmer), dinucleotide-based auto-cross covariance (DACC), and pseudo dinucleotide composition (PseDNC). These features are able to incorporate the nucleic acid composition and their order information into the predictor. The proposed SVM-EL achieves an accuracy of 82.89% on a widely used benchmark dataset, which outperforms some related methods.