Affordable Access

Publisher Website

iXora: exact haplotype inferencing and trait association

Authors
Journal
BMC Genetics
1471-2156
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Volume
14
Issue
1
Identifiers
DOI: 10.1186/1471-2156-14-48
Keywords
  • Methodology Article
Disciplines
  • Biology
  • Design

Abstract

Background We address the task of extracting accurate haplotypes from genotype data of individuals of large F1 populations for mapping studies. While methods for inferring parental haplotype assignments on large F1 populations exist in theory, these approaches do not work in practice at high levels of accuracy. Results We have designed iXora (Identifying crossovers and recombining alleles), a robust method for extracting reliable haplotypes of a mapping population, as well as parental haplotypes, that runs in linear time. Each allele in the progeny is assigned not just to a parent, but more precisely to a haplotype inherited from the parent. iXora shows an improvement of at least 15% in accuracy over similar systems in literature. Furthermore, iXora provides an easy-to-use, comprehensive environment for association studies and hypothesis checking in populations of related individuals. Conclusions iXora provides detailed resolution in parental inheritance, along with the capability of handling very large populations, which allows for accurate haplotype extraction and trait association. iXora is available for non-commercial use from http://researcher.ibm.com/project/3430.

There are no comments yet on this publication. Be the first to share your thoughts.

Statistics

Seen <100 times
0 Comments

More articles like this

Evaluating associations of haplotypes with traits.

on Genetic epidemiology December 2004

Associations between casein haplotypes and milk yi...

on Journal of Dairy Science September 1995

Power and sample size for testing associations of...

on Annals of Human Genetics January 2006
More articles like this..