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Nucleic Acids Research 2005 33(Database Issue):D442-D446; doi:10.1093/nar/gki094
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Nucleic Acids Research, 2005, Vol. 33, Database issue D442-D446
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

DED: Database of Evolutionary Distances

Vamsi Veeramachaneni and Wojciech Makalowski*

Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA

* To whom correspondence should be addressed at Department of Biology, Pennsylvania State University, 514 Mueller Lab, University Park, PA 16802, USA. Tel: +1 814 865 5025; Fax: +1 814 865 9366; Email: wojtek{at}psu.edu

Received August 15, 2004; Revised and Accepted October 12, 2004

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/.

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