DED: Database of Evolutionary Distances

Abstract

A large database of homologous sequence alignments with good estimates of evolutionary distances can be a valuable resource for molecular evolutionary studies and phylogenetic research in particular. We recently created a database containing 159 921 transcripts from human, mouse, rat, zebrafish and fugu species. Approximately 16 000 homology groups were identified with the help of Ensembl homology evidence. At the macro-level, the database allows us to answer queries of the form: (1) What is the average k-distance between 5′ untranslated regions of human and mouse? (2) List the 10 groups with the highest Ka/Ks ratio between mouse and rat. (3) List all identical proteins between human and rat. Researchers interested in specific proteins can use a simple web interface to retrieve the homology groups of interest, examine all pairwise distances between members of the group and study the conservation of exon-intron gene structures using a graphical interface. The database is available at http://warta.bio.psu.edu/DED/. © Oxford University Press 2005; all rights reserved.