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DED: Database of Evolutionary Distances.

Vamsi Veeramachaneni1, Wojciech Makalowski

  • 1Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.

Nucleic Acids Research
|December 21, 2004
PubMed
Summary
This summary is machine-generated.

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A new database offers evolutionary distance estimates for over 159,000 transcripts across five species. This resource aids molecular evolution and phylogenetic research by enabling complex sequence comparison queries.

Area of Science:

  • Genomics
  • Molecular Evolution
  • Bioinformatics

Background:

  • Homologous sequence alignments are crucial for understanding evolutionary relationships.
  • Estimating evolutionary distances aids phylogenetic research.
  • A comprehensive database facilitates large-scale molecular evolutionary studies.

Purpose of the Study:

  • To create a database of homologous sequence alignments for human, mouse, rat, zebrafish, and fugu.
  • To provide estimates of evolutionary distances for these species.
  • To develop a resource for molecular evolutionary and phylogenetic research.

Main Methods:

  • Collected 159,921 transcripts from five species.
  • Identified approximately 1,000 homology groups using Ensembl homology evidence.

Related Experiment Videos

  • Developed a web interface for querying evolutionary distances and gene structure conservation.

    • Main Results:

    • Established a database containing extensive homologous sequence data.
    • Enabled queries on average k-distances, K(a)/K(s) ratios, and identical protein identification.
    • Facilitated examination of pairwise distances and exon-intron structure conservation.

    Conclusions:

    • The created database is a valuable resource for molecular evolutionary studies.
    • The database supports phylogenetic research by providing evolutionary distance estimates.
    • The web interface allows researchers to explore homology groups and gene structure conservation effectively.