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    The adaptive evolution database (TAED).

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    The adaptive evolution database ...
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    Genre
    Journal Article
    Date
    2001-01-01
    Author
    Liberles, DA
    Schreiber, DR
    Govindarajan, S
    Chamberlin, SG
    Benner, SA
    Subject
    Adaptation, Physiological
    Animals
    Cattle
    Computational Biology
    Conserved Sequence
    Databases, Genetic
    Databases, Nucleic Acid
    Evolution, Molecular
    Genes
    Genetic Variation
    Likelihood Functions
    Mutagenesis
    Phylogeny
    Proteins
    Sequence Alignment
    Structure-Activity Relationship
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    Permanent link to this record
    http://hdl.handle.net/20.500.12613/5082
    
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    DOI
    10.1186/gb-2001-2-8-research0028
    Abstract
    BACKGROUND: The Master Catalog is a collection of evolutionary families, including multiple sequence alignments, phylogenetic trees and reconstructed ancestral sequences, for all protein-sequence modules encoded by genes in GenBank. It can therefore support large-scale genomic surveys, of which we present here The Adaptive Evolution Database (TAED). In TAED, potential examples of positive adaptation are identified by high values for the normalized ratio of nonsynonymous to synonymous nucleotide substitution rates (KA/KS values) on branches of an evolutionary tree between nodes representing reconstructed ancestral sequences. RESULTS: Evolutionary trees and reconstructed ancestral sequences were extracted from the Master Catalog for every subtree containing proteins from the Chordata only or the Embryophyta only. Branches with high KA/KS values were identified. These represent candidate episodes in the history of the protein family when the protein may have undergone positive selection, where the mutant form conferred more fitness than the ancestral form. Such episodes are frequently associated with change in function. An unexpectedly large number of families (between 10% and 20% of those families examined) were found to have at least one branch with high KA/KS values above arbitrarily chosen cut-offs (1 and 0.6). Most of these survived a robustness test and were collected into TAED. CONCLUSIONS: TAED is a raw resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study. It can be expanded to include other evolutionary information (for example changes in gene regulation or splicing) placed in a phylogenetic perspective.
    Citation to related work
    Springer Science and Business Media LLC
    Has part
    Genome biology
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    ae974a485f413a2113503eed53cd6c53
    http://dx.doi.org/10.34944/dspace/5064
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