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NRSub: a non-redundant database for Bacillus subtilis

G Perrière1, I Moszer, T Gojobori

  • 1Laboratoire de Biometrie, Universite Claude Bernard-Lyon, Villeurbanne, France.

Nucleic Acids Research
|January 1, 1996
PubMed
Summary

A new Bacillus subtilis genome database, NRSub, integrates existing sequence data. This non-redundant, annotated resource enhances genomic research and accessibility for scientists worldwide.

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Bacillus subtilis whole genome sequencing is an international research effort.
  • Existing sequence collections (EMBL, GenBank, DDBJ) contain redundant data.
  • A unified, non-redundant database is crucial for efficient genomic analysis.

Purpose of the Study:

  • To develop a comprehensive, non-redundant, and fully annotated sequence database for Bacillus subtilis.
  • To integrate and enhance existing Bacillus subtilis sequence information.
  • To facilitate access to curated genomic data.

Main Methods:

  • Consolidation of Bacillus subtilis sequences from EMBL, GenBank, and DDBJ.
  • Identification and removal of redundant sequences.
  • Addition of detailed annotations including gene accession numbers, genetic map locations, and codon usage.
  • Cross-referencing with external databases (EMBL, MEDLINE, SWISS-PROT, ENZYME).
  • Merging of NRSub and SubtiList databases, ensuring identical sequence contigs.

Main Results:

  • Creation of NRSub, a non-redundant, fully annotated Bacillus subtilis sequence database.
  • Enhanced annotation including gene information, genetic map positions, and codon usage.
  • Integration of cross-references to major biological databases.
  • Distribution of NRSub in EMBL flatfile and ACNUC formats, and SubtiList as a 4th Dimension relational database.
  • Accessibility via dedicated World Wide Web servers in France and Japan.

Conclusions:

  • The NRSub database provides a valuable, curated resource for Bacillus subtilis genomics.
  • Enhanced annotation and cross-referencing improve data utility for researchers.
  • Accessible distribution formats and web servers promote widespread use in the scientific community.

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