Gene Mapping, Discovery, and Expression pp 9-20

Part of the Methods in Molecular Biology book series (MIMB, volume 338)

Methods for Identifying and Mapping Recent Segmental and Gene Duplications in Eukaryotic Genomes

  • Razi Khaja
  • Jeffrey R. MacDonald
  • Junjun Zhang
  • Stephen W. Scherer

Abstract

The aim of this chapter is to provide instruction for analyzing and mapping recent segmental and gene duplications in eukaryotic genomes. We describe a bioinformatics-based approach utilizing computational tools to manage eukaryotic genome sequences to characterize and understand the evolutionary fates and trajectories of duplicated genes. An introduction to bioinformatics tools and programs such as BLAST, Perl, BioPerl, and the GFF specification provides the necessary background to complete this analysis for any eukaryotic genome of interest.

Key Words

Bioinformatics BLAST/MegaBLAST gene duplication gene ontology genome assembly genomic disorder GFF (Generic Feature Format) homology neofunctionalization paralogous Perl/BioPerl pseudogene RefSeq RepeatMasker segmental duplication sequence alignments subfunctionalization 

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Copyright information

© Humana Press Inc. 2006

Authors and Affiliations

  • Razi Khaja
    • 1
  • Jeffrey R. MacDonald
    • 1
  • Junjun Zhang
    • 2
  • Stephen W. Scherer
    • 1
  1. 1.Program in Genetics and Genomic Biology, Research InstituteThe Hospital for Sick ChildrenTorontoCanada
  2. 2.The Hospital for Sick ChildrenTorontoCanada

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