DED: Database of Evolutionary Distances.
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/.
Veeramachaneni
Vamsi
V
Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
Makalowski
Wojciech
W
D020121:5' Untranslated Regions; D000818:Animals; D030541:Databases, Genetic; D019143:Evolution, Molecular; D006801:Humans; D051379:Mice; D010802:Phylogeny; D011506:Proteins / Q000145:classification / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry / Q000145:classification; D051381:Rats; D017385:Sequence Homology; D023741:Takifugu / Q000235:genetics; D014584:User-Computer Interface; D015027:Zebrafish / Q000235:genetics
D020121:5' Untranslated Regions; D011506:Proteins; D012333:RNA, Messenger