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Nucleic Acids Research 2005 33(Database Issue):D495-D497; doi:10.1093/nar/gki090
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Nucleic Acids Research, 2005, Vol. 33, Database issue D495-D497
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics

Christian Roth, Matthew J. Betts, Pär Steffansson, Gisle Sælensminde and David A. Liberles*

Computational Biology Unit, BCCS, University of Bergen, 5020 Bergen, Norway

* To whom correspondence should be addressed. Tel: +47 55584043; Fax: +47 55584295; Email: liberles{at}cbu.uib.no

Received August 14, 2004; Revised and Accepted October 12, 2004

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.

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