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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