Format

Send to

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2009 Jun 15;25(12):i231-9. doi: 10.1093/bioinformatics/btp229.

Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data.

Author information

1
Computer Science Division and Department of Statistics, University of California, Berkeley, CA, USA.

Abstract

MOTIVATION:

Two known types of meiotic recombination are crossovers and gene conversions. Although they leave behind different footprints in the genome, it is a challenging task to tease apart their relative contributions to the observed genetic variation. In particular, for a given population SNP dataset, the joint estimation of the crossover rate, the gene conversion rate and the mean conversion tract length is widely viewed as a very difficult problem.

RESULTS:

In this article, we devise a likelihood-based method using an interleaved hidden Markov model (HMM) that can jointly estimate the aforementioned three parameters fundamental to recombination. Our method significantly improves upon a recently proposed method based on a factorial HMM. We show that modeling overlapping gene conversions is crucial for improving the joint estimation of the gene conversion rate and the mean conversion tract length. We test the performance of our method on simulated data. We then apply our method to analyze real biological data from the telomere of the X chromosome of Drosophila melanogaster, and show that the ratio of the gene conversion rate to the crossover rate for the region may not be nearly as high as previously claimed.

AVAILABILITY:

A software implementation of the algorithms discussed in this article is available at http://www.cs.berkeley.edu/ approximately yss/software.html.

PMID:
19477993
PMCID:
PMC2687983
DOI:
10.1093/bioinformatics/btp229
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems Icon for PubMed Central
    Loading ...
    Support Center