title: Recombination spot identification Based on gapped k-mers.
abstract: Recombination is crucial for biological evolution, which provides many new combinations of genetic diversity. Accurate identification of recombination spots is useful for DNA function study. To improve the prediction accuracy, researchers have proposed several computational methods for recombination spot identification. The k-mer feature is one of the most useful features for modeling the properties and function of DNA sequences. However, it suffers from the inherent limitation. If the value of word length k is large, the occurrences of k-mers are closed to a binary variable, with a few k-mers present once and most k-mers are absent. This usually causes the sparse problem and reduces the classification accuracy. To solve this problem, we add gaps into k-mer and introduce a new feature called gapped k-mer (GKM) for identification of recombination spots. By using this feature, we present a new predictor called SVM-GKM, which combines the gapped k-mers and Support Vector Machine (SVM) for recombination spot identification. Experimental results on a widely used benchmark dataset show that SVM-GKM outperforms other highly related predictors. Therefore, SVM-GKM would be a powerful predictor for computational genomics.
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China.
authors.forename: Rong
authors.initials: R
authors.lastname: Wang
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Xu
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D019985:Benchmarking; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D006801:Humans; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D012984:Software; D060388:Support Vector Machine
chemical_list: D004247:DNA