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MicrobeDB: a locally maintainable database of microbial genomic sequences.

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requires the general organization and comparison of tens to thousands of genomes both from public repositories and unpublished sources.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.MicrobeDB is freely available under the GNU-GPL at: http://github.com/mlangill/microbedb/

SUBMITTER: Langille MG

PROVIDER: S-EPMC3389766 | biostudies-other | 2012 Jul

REPOSITORIES: biostudies-other

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MicrobeDB: a locally maintainable database of microbial genomic sequences.

Langille Morgan G I MG Laird Matthew R MR Hsiao William W L WW Chiu Terry A TA Eisen Jonathan A JA Brinkman Fiona S L FS

Bioinformatics (Oxford, England) 20120509 14

<h4>Unlabelled</h4>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requires the general organization and comparison of tens to thousands of genomes both from public repositories and unpublished sources.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 progra ...[more]

PMID: 22576174

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