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    Evolutionary sequence analysis of complete eukaryote genomes

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    Evolutionary sequence analysis ...
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    Genre
    Review
    Journal
    Date
    2005-03-11
    Author
    Blair, JE
    Shah, P
    Hedges, SB
    Subject
    Animals
    Biodiversity
    Biological Evolution
    Computational Biology
    Databases, Genetic
    Databases, Protein
    Eukaryotic Cells
    Evolution, Molecular
    Fossils
    Gene Duplication
    Genome
    Genome, Archaeal
    Humans
    Models, Genetic
    Phylogeny
    Programming Languages
    Proteins
    Sequence Analysis
    Sequence Analysis, DNA
    Sequence Analysis, Protein
    Software
    Time Factors
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    Permanent link to this record
    http://hdl.handle.net/20.500.12613/5650
    
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    DOI
    10.1186/1471-2105-6-53
    Abstract
    Background: Gene duplication and gene loss during the evolution of eukaryotes have hindered attempts to estimate phylogenies and divergence times of species. Although current methods that identify clusters of orthologous genes in complete genomes have helped to investigate gene function and gene content, they have not been optimized for evolutionary sequence analyses requiring strict orthology and complete gene matrices. Here we adopt a relatively simple and fast genome comparison approach designed to assemble orthologs for evolutionary analysis. Our approach identifies single-copy genes representing only species divergences (panorthologs) in order to minimize potential errors caused by gene duplication. We apply this approach to complete sets of proteins from published eukaryote genomes specifically for phylogeny and time estimation. Results: Despite the conservative criterion used, 753 panorthologs (proteins) were identified for evolutionary analysis with four genomes, resulting in a single alignment of 287,000 amino acids. With this data set, we estimate that the divergence between deuterostomes and arthropods took place in the Precambrian, approximately 400 million years before the first appearance of animals in the fossil record. Additional analyses were performed with seven, 12, and 15 eukaryote genomes resulting in similar divergence time estimates and phylogenies. Conclusion: Our results with available eukaryote genomes agree with previous results using conventional methods of sequence data assembly from genomes. They show that large sequence data sets can be generated relatively quickly and efficiently for evolutionary analyses of complete genomes. © 2005 Blair et al; licensee BioMed Central Ltd.
    Citation to related work
    Springer Science and Business Media LLC
    Has part
    BMC Bioinformatics
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    ae974a485f413a2113503eed53cd6c53
    http://dx.doi.org/10.34944/dspace/5632
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