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GOBASE: the organelle genome database.

N Shimko1, L Liu, B F Lang

  • 1Program in Evolutionary Biology, Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, Québec, H3T 1J4, Canada.

Nucleic Acids Research
|January 11, 2000
PubMed
Summary

GOBASE is a unique biological database for organelle data, focusing on validated mitochondrial sequences, structures, and genetic maps. It provides comprehensive, expert-verified information for broad taxonomic groups, aiding biological research.

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Organelle data, particularly mitochondrial information, is diverse and requires expert curation.
  • Existing biological databases may lack comprehensive, validated data across broad taxonomic ranges.

Purpose of the Study:

  • To introduce GOBASE, a novel biological database.
  • To consolidate and present verified organelle data, with an initial focus on mitochondrial information.
  • To enable sophisticated biological queries through an integrated database structure.

Main Methods:

  • Integrated diverse biological data on organelles, including nucleotide and protein sequences, RNA secondary structures, and genetic maps.
  • Focused on mitochondrial data with broad taxonomic coverage.

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  • Implemented a relational database management system with an object-oriented view via a WWW interface.
  • Developed specialized software for database curation, including data updates, validation, and correction.

    • Main Results:

    • GOBASE now contains comprehensive, expert-verified mitochondrial data, including sequences, structures, genetic maps, and taxonomic/organismal information.
    • The database structure allows for sophisticated biological queries.
    • Data validation, completion, correction, and standardization have been prioritized.
    • Missing critical data, such as genetic maps and RNA secondary structures, have been generated and added.

    Conclusions:

    • GOBASE serves as a valuable, unique resource for organelle research, particularly for mitochondrial data.
    • The database's emphasis on data quality and accessibility facilitates meaningful biological analysis.
    • The integrated and curated nature of GOBASE supports advanced biological research and discovery.