Microbedb

A locally maintainable database of microbial genomic sequences

Morgan G I Langille, Matthew R. Laird, William W L Hsiao, Terry A. Chiu, Jonathan A Eisen, Fiona S L Brinkman

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

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requires the general organization and comparison of tens to thousands of genomes both from public repositories and unpublished sources.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.

Original languageEnglish (US)
Article numberbts273
Pages (from-to)1947-1948
Number of pages2
JournalBioinformatics
Volume28
Issue number14
DOIs
StatePublished - Jul 2012

Fingerprint

Genomics
Genome
Archaeal Genome
Genes
Microbial Genome
Databases
Bacterial Genomes
Automation
Comparative Genomics
Parsing
Repository
Annotation
Programming
Resources
Interaction

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Langille, M. G. I., Laird, M. R., Hsiao, W. W. L., Chiu, T. A., Eisen, J. A., & Brinkman, F. S. L. (2012). Microbedb: A locally maintainable database of microbial genomic sequences. Bioinformatics, 28(14), 1947-1948. [bts273]. https://doi.org/10.1093/bioinformatics/bts273

Microbedb : A locally maintainable database of microbial genomic sequences. / Langille, Morgan G I; Laird, Matthew R.; Hsiao, William W L; Chiu, Terry A.; Eisen, Jonathan A; Brinkman, Fiona S L.

In: Bioinformatics, Vol. 28, No. 14, bts273, 07.2012, p. 1947-1948.

Research output: Contribution to journalArticle

Langille, MGI, Laird, MR, Hsiao, WWL, Chiu, TA, Eisen, JA & Brinkman, FSL 2012, 'Microbedb: A locally maintainable database of microbial genomic sequences', Bioinformatics, vol. 28, no. 14, bts273, pp. 1947-1948. https://doi.org/10.1093/bioinformatics/bts273
Langille MGI, Laird MR, Hsiao WWL, Chiu TA, Eisen JA, Brinkman FSL. Microbedb: A locally maintainable database of microbial genomic sequences. Bioinformatics. 2012 Jul;28(14):1947-1948. bts273. https://doi.org/10.1093/bioinformatics/bts273
Langille, Morgan G I ; Laird, Matthew R. ; Hsiao, William W L ; Chiu, Terry A. ; Eisen, Jonathan A ; Brinkman, Fiona S L. / Microbedb : A locally maintainable database of microbial genomic sequences. In: Bioinformatics. 2012 ; Vol. 28, No. 14. pp. 1947-1948.
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