Estimating recombination rate distribution by optimal quantization

Evolution biologists are interested in a high resolution recombination map that depicts accurately how often a recombination event occurs at a specific location in the genome. With the availability of human genome physical map and fast sequencing technology, people start to estimate recombination rate distributions. We obtain recombination rate distribution functions for all the chromosomes in the human genome using an optimal quantization method. In this method, we are able to control explicitly 1 over-fitting/under-fitting. The obtained piece-wise constant recombination rate distribution functions are convenient to store and retrieve. Our experimental results showed more abrupt distribution functions than two recently published results. In the previous results, the over-/under-fitting issues were not addressed explicitly. We also had better quantitative performance than the Parzen window used in a previous approach. It suggests that the optimal quantization might be of great advantage for other genome feature distribution estimation.