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Generating Whole Bacterial Genomes from Clinical Samples using a Target Enrichment Workflow
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Published on: August 15, 2025

GeneDB--an annotation database for pathogens.

Flora J Logan-Klumpler1, Nishadi De Silva, Ulrike Boehme

  • 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. fl2@sanger.ac.uk

Nucleic Acids Research
|November 26, 2011
PubMed
Summary
This summary is machine-generated.

GeneDB is a comprehensive genome database for pathogens, offering curated annotation and sequence data. It features updated tools and a redesigned interface for improved usability in genomic research.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Pathogen Research

Background:

  • GeneDB serves as a vital genome database for prokaryotic and eukaryotic pathogens.
  • It centralizes genome sequence and annotation data, primarily from the Wellcome Trust Sanger Institute's Pathogen Genomics group.
  • The resource integrates data from both completed and ongoing genome projects.

Purpose of the Study:

  • To provide a user-friendly web portal for accessing pathogen genome data.
  • To enhance database-driven annotation tools and pipelines.
  • To accommodate frequent genome assembly updates and improve overall usability.

Main Methods:

  • Utilizing current web technologies for a significant website redesign.
  • Implementing database-driven annotation tools and pipelines.
  • Incorporating manually curated data from scientific literature and other sources.

Main Results:

  • The current release supports 41 datasets, with 17 manually curated by biologists.
  • Improved usability and accessibility through a redesigned web interface.
  • Integration of updated genome assemblies and annotation data.

Conclusions:

  • GeneDB is a key resource for pathogen genome production and annotation.
  • The database facilitates access to curated genomic information for researchers.
  • Ongoing development ensures GeneDB remains a valuable tool in infectious disease research.