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Database Commons - DED

DED

Citations: 6

z-index 0.00

Short name DED
Full name Database of Evolutionary Distances
Description DED is a large database of homologous sequence alignments with good estimates of evolutionary distances for molecular evolutionary studies and phylogenetic research.
URL http://warta.bio.psu.edu/DED/
Year founded 2005
Last update & version     
Availability Not Available
University/Institution hosted University Park
Address Pennsylvania State University, University Park, PA 16802, USA
City University Park
Province/State PA
Country/Region United States
Contact name Wojciech MakaƂowski
Contact email wojtek@psu.edu
Data type(s)
Major organism(s)
Keyword(s)
  • evolutionary distances
  • homologous sequence alignments
Publication(s)
  • DED: Database of Evolutionary Distances. [PMID: 15608234]

    Vamsi Veeramachaneni, Wojciech Makalowski
    Nucleic acids research 2005:33(Database issue)
    6 Citations (Google Scholar as of 2016-01-28)

    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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Tags

DNA
Danio rerio Homo sapiens Mus musculus Rattus norvegicus
evolutionary distances homologous sequence alignments

Record metadata

  • Created on: 2015-07-13
  • Curated by:
    • Jian Sang [2016-04-04]
    • Mengwei Li [2016-02-20]
    • Jian Sang [2015-12-06]
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