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dc.creatorBlair, JE
dc.creatorShah, P
dc.creatorHedges, SB
dc.date.accessioned2021-02-01T22:25:24Z
dc.date.available2021-02-01T22:25:24Z
dc.date.issued2005-03-11
dc.identifier.issn1471-2105
dc.identifier.issn1471-2105
dc.identifier.doihttp://dx.doi.org/10.34944/dspace/5632
dc.identifier.other15762985 (pubmed)
dc.identifier.urihttp://hdl.handle.net/20.500.12613/5650
dc.description.abstractBackground: 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.
dc.format.extent53-53
dc.language.isoeng
dc.relation.haspartBMC Bioinformatics
dc.relation.isreferencedbySpringer Science and Business Media LLC
dc.rightsCC BY
dc.subjectAnimals
dc.subjectBiodiversity
dc.subjectBiological Evolution
dc.subjectComputational Biology
dc.subjectDatabases, Genetic
dc.subjectDatabases, Protein
dc.subjectEukaryotic Cells
dc.subjectEvolution, Molecular
dc.subjectFossils
dc.subjectGene Duplication
dc.subjectGenome
dc.subjectGenome, Archaeal
dc.subjectHumans
dc.subjectModels, Genetic
dc.subjectPhylogeny
dc.subjectProgramming Languages
dc.subjectProteins
dc.subjectSequence Analysis
dc.subjectSequence Analysis, DNA
dc.subjectSequence Analysis, Protein
dc.subjectSoftware
dc.subjectTime Factors
dc.titleEvolutionary sequence analysis of complete eukaryote genomes
dc.typeArticle
dc.type.genreReview
dc.type.genreJournal
dc.relation.doi10.1186/1471-2105-6-53
dc.ada.noteFor Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.edu
dc.date.updated2021-02-01T22:25:21Z
refterms.dateFOA2021-02-01T22:25:24Z


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