Support system for linkage analysis using Java language and HORB

Yasuhiko Wada and Hiroshi Yasue

Dep. Animal Breeding and Genetics
National Institute of Animal Industry
2 Ikenodai, Kukisaki-machi, Inashiki-gun,
Ibaraki 305-0901, Japan

Summary

  In order to explore genes or genetic regions responsible for traits,
livestock resource populations have been constructed and used for
linkage analysis between traits and genetic markers. For linkage 
analysis, more than a thousand genetic markers have been developed
in swine and cattle, and the allele type of each marker has been
determined in individuals among populations by genotyping systems
such as GeneScan672 (Applied Biosystems, USA).

  However, empirically the genotyping systems risk generation of 
erros in allele typing at a given frequency, which in turn results
in elongated linkage maps and assignment errors for trait loci.
Mistakes of allele typing often result in apparent chromosomal 
recombination in F2 animals. So if double or more recombinations
in a limited chromosomal region are detected, a re-examination of 
the allele typing data becomes necessary. In the present study,
we have developed a support system for linkage analysis using
Java language and HORB (Hirano 1997), which has a feature to display
chromosomal recombinations of F2 animals and evident errors of 
allele typing graphically in the applet. The system was constructed
with the Java language based on the JDK1.1. With the applet viewer
JDK1.1.x, users can access the demo applet of the system (http://
ws4.niai.affrc.go.jp/linkagent/).

Japanese Journal of Computer Science 6(1), 11-17 (1999)