MicrobeDB: a locally maintainable database of microbial genomic sequences

Bioinformatics. 2012 Jul 15;28(14):1947-8. doi: 10.1093/bioinformatics/bts273. Epub 2012 May 9.


Analysis of microbial genomes often requires the general organization and comparison of tens to thousands of genomes both from public repositories and unpublished sources. MicrobeDB provides a foundation for such projects by the automation of downloading published, completed bacterial and archaeal genomes from key sources, parsing annotations of all genomes (both public and private) into a local database, and allowing interaction with the database through an easy to use programming interface. MicrobeDB creates a simple to use, easy to maintain, centralized local resource for various large-scale comparative genomic analyses and a back-end for future microbial application design.

Availability: MicrobeDB is freely available under the GNU-GPL at: http://github.com/mlangill/microbedb/

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods
  • Databases, Genetic*
  • Genome, Archaeal*
  • Genome, Bacterial*
  • Genomics
  • Internet
  • Software
  • User-Computer Interface