title: Using weighted features to predict recombination hotspots in Saccharomyces cerevisiae.
abstract: Characterization and accurate prediction of recombination hotspots and coldspots have crucial implications for the mechanism of recombination. Several models have predicted recombination hot/cold spots successfully, but there is still much room for improvement. We present a novel classifier in which k-mer frequency, physical and thermodynamic properties of DNA sequences are incorporated in the form of weighted features. Applying the classifier to recombination hot/cold ORFs in Saccharomyces cerevisiae, we achieved an accuracy of 90%, which is ~5% higher than existing methods, such as iRSpot-PseDNC, IDQD and Random Forest. The model also predicted non-ORF recombination hot/cold spots sequences in S. cerevisiae with high accuracy. A broad applicability of the model in the field of classification is expected.
authors.affiliation: School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou 014010, China; The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China.
authors.forename: Guoqing
authors.initials: G
authors.lastname: Liu
authors.affiliation: School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou 014010, China; The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China.
authors.forename: Yongqiang
authors.initials: Y
authors.lastname: Xing
authors.affiliation: School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou 014010, China; The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Cai
mesh_terms: D001483:Base Sequence; D016366:Open Reading Frames / Q000235:genetics; D011995:Recombination, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D013816:Thermodynamics
keywords: Dinucleotide flexibility; Recombination hotspots; Thermodynamic properties; Weighted features