The Adaptive Evolution Database (TAED): A phylogeny based tool for comparative genomics
Genre
Journal ArticleDate
2005-01-01Author
Roth, CBetts, MJ
Steffansson, P
Sælensminde, G
Liberles, DA
Subject
AnimalsChordata
Computer Graphics
Database Management Systems
Databases, Genetic
Evolution, Molecular
Genome
Genomics
Phylogeny
Plants
Sequence Alignment
Permanent link to this record
http://hdl.handle.net/20.500.12613/6117
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10.1093/nar/gki090Abstract
From 138 662 embryophyte (higher plant) and 348 142 chordate genes, 4216 embryophyte and 15 452 chordate gene families were generated. For each of these gene families, multiple sequence alignments, phylogenetic trees, ratios of non-synonymous to synonymous nucleotide substitution rates (Ka/Ks), mappings from gene trees to the NCBI taxonomy and structural links to solved three-dimensional protein structures in the Protein Data Bank (PDB) with Grantham-weighted mutational factors were all calculated. Of the 'gene family trees', 173 embryophyte and 505 chordate branches show Ka/Ks ≫ 1 and are candidates for functional adaptation. The calculated information is available both as a gene family database and as a phylogenetically indexed resource, called 'The Adaptive Evolution Database' (TAED), available at http://www.bioinfo.no /tools/TAED. © Oxford University Press 2005; all rights reserved.Citation to related work
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http://dx.doi.org/10.34944/dspace/6099