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The PEDANT genome database.

Dmitrij Frishman1, Martin Mokrejs, Denis Kosykh

  • 1Institute for Bioinformatics, GSF - National Research Center for Environment and Health, Ingolstädter Landstrasse 1, 85764 Neueherberg, Germany. d.frishman@gsf.de

Nucleic Acids Research
|January 10, 2003
PubMed
Summary
This summary is machine-generated.

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The PEDANT genome database offers comprehensive bioinformatics analysis for 177 genomes, including human and mouse. New features enhance genome comparison and protein function prediction for structural genomics.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • The PEDANT genome database provides automated analysis of genomic sequences using various bioinformatics tools.
  • It currently includes 177 completely sequenced and unfinished genomes, encompassing large eukaryotic genomes like human and mouse.

Purpose of the Study:

  • To describe the current status of the PEDANT database.
  • To highlight novel analytical features added to the PEDANT server in 2002.

Main Methods:

  • Integration with the BioRS data retrieval system for efficient text queries.
  • Pre-computation of sequence clusters within each complete genome.
  • Implementation of genome comparison tools, including comparison tables and protein function prediction based on genomic context.

Related Experiment Videos

  • Computation and visualization of protein-protein interaction (PPI) networks using experimental data.

    • Main Results:

    • The PEDANT database now offers enhanced genome comparison capabilities.
    • Protein function prediction is improved through genomic context analysis.
    • Protein-protein interaction networks can be computed and visualized.
    • Functional and structural predictions are available for 650,000 genomic proteins.

    Conclusions:

    • PEDANT serves as a valuable resource for functional and structural genomics.
    • The updated features enhance the utility of PEDANT for genomic research.