Abstract
Meiotic recombination is non-uniformly distributed across the genome, occurring at relatively high frequencies in some genomic regions (hotspots) and at relatively low frequencies in others (coldspots). Recombination depends not only on sequence features, but also on chromatin structure. Accurate identification of recombination hotspots and coldspots would assist our understanding of genetic recombination mechanisms and genome evolution. In this study, 2 kb recombination hot/cold spots were identified in Saccharomyces cerevisiae from experimental data. Using increment diversity with quadratic discriminant (IDQD) and support vector machine (SVM) algorithms, we predicted hot/cold spots from multiple genomic features associated with sequence, structure, thermodynamic stability of DNA and chromatin structure. The predictive model accurately discriminated recombination hotspots from coldspots. IDQD yielded higher overall performance than SVM in terms of sensitivity, specificity and accuracy.
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