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PubMed · 15608234

DED: Database of Evolutionary Distances.

Vamsi Veeramachaneni·Wojciech Makalowski
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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 1,000 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 K(a)/K(s) 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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5' Untranslated RegionsAnimalsDatabases, GeneticEvolution, MolecularHumansMicePhylogenyProteinsRNA, MessengerRatsSequence HomologyTakifuguUser-Computer InterfaceZebrafishJournal Article

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Vamsi Veeramachaneni, Wojciech Makalowski. 2005-01-01. DED: Database of Evolutionary Distances.. https://doi.org/10.1093/nar%2Fgki094

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