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Background: Meiotic recombination does not occur evenly across the genome, but instead occurs at relatively high frequencies in some genomic regions (hotspots) and relatively low frequencies in others (coldspots).Recombination depends not only on scquencc features, but also on chromatin structure.Identification and characterization of hotspots and coldspots are considerably significant for that information about hotspots/coldspots would shed light on the mechanism of recombination and genome evolution.Determination of high-resolution recombination rates using genetic experiments is time-consuming and expensive.Thus, it is necessary to develop computational methods to predict recombination rates or recombination hotspots in the genome.So far, there is no model for predicting recombination hotspots in which chromatin structure is incorporated.In this study, we analyzed the correlation between recombination and nucleosome occupancy, and presented a model for predicting recombination hotspots based on the sequence and nucleosome occupancy in yeast.Methods: The relationship between recombination and nucleosome occupancy is estimated by Pearson correlation.A model based on IDQD (increment of diversity combined with quadratic discriminant) algorithm using tetranucleotide frequencies in sequences and nucleosome occupancy as features is developed to predict recombination hotspots/coldspots in yeast.Results: Our results show that the regions with high nucleosome occupancy have high recombination rate in the yeast genome.Pearson correlation between genome-wide recombination rate and nucleosome occupancy is significant (R=0.151, P<0.001).The prediction accuracy of hotspots based on sequence alone is 80%.The prediction accuracy increased to 81.6% when nucleosome occupancy is used as an additional feature.Conclusion: Our data show that recombination is significantly positively correlated with nucleosome occupancy in the yeast genome, and hotspots prediction accuracy is improved when nucleosome occupancy is used as an additional feature in the IDQD-based prediction model.Our results indicate that chromatin structure, apart from DNA sequence, is another factor which has significant effect on meiotic recombination in yeast .