title: Sequence-based identification of recombination spots using pseudo nucleic acid representation and recursive feature extraction by linear kernel SVM.
abstract: BACKGROUND
  Identification of the recombination hot/cold spots is critical for understanding the mechanism of recombination as well as the genome evolution process. However, experimental identification of recombination spots is both time-consuming and costly. Developing an accurate and automated method for reliably and quickly identifying recombination spots is thus urgently needed.
  
  
  RESULTS
  Here we proposed a novel approach by fusing features from pseudo nucleic acid composition (PseNAC), including NAC, n-tier NAC and pseudo dinucleotide composition (PseDNC). A recursive feature extraction by linear kernel support vector machine (SVM) was then used to rank the integrated feature vectors and extract optimal features. SVM was adopted for identifying recombination spots based on these optimal features. To evaluate the performance of the proposed method, jackknife cross-validation test was employed on a benchmark dataset. The overall accuracy of this approach was 84.09%, which was higher (from 0.37% to 3.79%) than those of state-of-the-art tools.
  
  
  CONCLUSIONS
  Comparison results suggested that linear kernel SVM is a useful vehicle for identifying recombination hot/cold spots.
authors.forename: Liqi
authors.initials: L
authors.lastname: Li
authors.forename: Sanjiu
authors.initials: S
authors.lastname: Yu
authors.forename: Weidong
authors.initials: W
authors.lastname: Xiao
authors.forename: Yongsheng
authors.initials: Y
authors.lastname: Li
authors.forename: Lan
authors.initials: L
authors.lastname: Huang
authors.affiliation: Department of General Surgery, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China. xqzheng@shnu.edu.cn.
authors.forename: Xiaoqi
authors.initials: X
authors.lastname: Zheng
authors.forename: Shiwen
authors.initials: S
authors.lastname: Zhou
authors.forename: Hua
authors.initials: H
authors.lastname: Yang
mesh_terms: D004247:DNA / Q000737:chemistry / Q000235:genetics; D009696:Nucleic Acids / Q000737:chemistry; D011995:Recombination, Genetic; D012984:Software; D060388:Support Vector Machine
chemical_list: D009696:Nucleic Acids; D004247:DNA