The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics.
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 (K(a)/K(s)), 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 K(a)/K(s) >> 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.
Roth
Christian
C
Computational Biology Unit, BCCS, University of Bergen, 5020 Bergen, Norway.
Betts
Matthew J
MJ
Steffansson
Pär
P
Saelensminde
Gisle
G
Liberles
David A
DA
D000818:Animals; D043344:Chordata; D003196:Computer Graphics; D003628:Database Management Systems; D030541:Databases, Genetic; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics; D010802:Phylogeny; D010944:Plants / Q000235:genetics; D016415:Sequence Alignment