Razi Khaja Jeffrey R Mac Donald Junjun Zhang and Stephen W Scherer


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; neofunc-tionalization; paralogous; Perl/BioPerl; pseudogene; RefSeq; RepeatMasker; segmental duplication; sequence alignments; subfunctionalization.

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