Estimating recombination rate distribution by optimal quantization

M. Song, Stephane Boissinot, R. M. Haralick, I. T. Phillips

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We obtain recombination rate distribution functions for all human chromosomes using an optimal quantization method. This nonparametric method allows us to control over-/under-fitting. The 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. Our estimation had greater log likelihood over a previous result using Parzen window. It suggests that the optimal quantization technique might be of great advantage for estimation of other genomic feature distributions.

Original languageEnglish (US)
Title of host publicationProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages403-406
Number of pages4
ISBN (Electronic)0769520006, 9780769520001
DOIs
StatePublished - Jan 1 2003
Event2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States
Duration: Aug 11 2003Aug 14 2003

Other

Other2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
CountryUnited States
CityStanford
Period8/11/038/14/03

Fingerprint

Distribution functions
Chromosomes

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Computer Science Applications

Cite this

Song, M., Boissinot, S., Haralick, R. M., & Phillips, I. T. (2003). Estimating recombination rate distribution by optimal quantization. In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003 (pp. 403-406). [1227346] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CSB.2003.1227346

Estimating recombination rate distribution by optimal quantization. / Song, M.; Boissinot, Stephane; Haralick, R. M.; Phillips, I. T.

Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. p. 403-406 1227346.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Song, M, Boissinot, S, Haralick, RM & Phillips, IT 2003, Estimating recombination rate distribution by optimal quantization. in Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003., 1227346, Institute of Electrical and Electronics Engineers Inc., pp. 403-406, 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003, Stanford, United States, 8/11/03. https://doi.org/10.1109/CSB.2003.1227346
Song M, Boissinot S, Haralick RM, Phillips IT. Estimating recombination rate distribution by optimal quantization. In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc. 2003. p. 403-406. 1227346 https://doi.org/10.1109/CSB.2003.1227346
Song, M. ; Boissinot, Stephane ; Haralick, R. M. ; Phillips, I. T. / Estimating recombination rate distribution by optimal quantization. Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. pp. 403-406
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