Gecko and GhostFam

Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes
  • Thomas Schmidt
  • Jens Stoye
Part of the Methods In Molecular Biology™ book series (MIMB, volume 396)

Summary

A popular approach in comparative genomics is to locate groups or clusters of orthologous genes in multiple genomes and to postulate functional association between the genes contained in such clusters. For a rigorous and efficient detection in multiple genomes, it is essential to have an appropriate model of gene clusters accompanied by efficient algorithms locating them. The Gecko method described herein was designed to serve as a basic tool for the detection and visualization of gene cluster data in prokaryotic genomes founded on a formal string-based gene cluster model.

Key Words

Comparative genomics gene cluster Gecko GhostFam common intervals 

Notes

Acknowledgments

The authors wish to thank Christian Rückert and Jörn Kalinowski for their helpful discussions on the topic of gene clusters and their valuable feedback during the development of GhostFam and Gecko.

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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Thomas Schmidt
    • 1
  • Jens Stoye
    • 2
  1. 1.Technische Fakultät, Universitat Bielefeld, International NRW Graduate School in Bioinformatics and Genome ResearchGermany
  2. 2.Technische Fakultät, Universitat BielefeldGermany

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