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Gene Mapping, Discovery, and Expression

Volume 338 of the series Methods in Molecular Biology pp 9-20

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

  • Razi KhajaAffiliated withProgram in Genetics and Genomic Biology, Research Institute, The Hospital for Sick Children
  • , Jeffrey R. MacDonaldAffiliated withProgram in Genetics and Genomic Biology, Research Institute, The Hospital for Sick Children
  • , Junjun ZhangAffiliated withThe Hospital for Sick Children
  • , Stephen W. SchererAffiliated withProgram in Genetics and Genomic Biology, Research Institute, The Hospital for Sick Children

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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