MicrobeDB: a locally maintainable database of microbial genomic sequences.

Bioinformatics
Morgan G I LangilleFiona S L Brinkman

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requires the general organization and comparison of tens to thousands of genomes both from public repositories and unpublished sources.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

References

Oct 9, 2002·Genome Research·Lincoln D SteinSuzanna Lewis
Jul 25, 2007·Bioinformatics·Christopher J MungallUNKNOWN FlyBase Consortium
Feb 12, 2008·BMC Genomics·Ramy K AzizOlga Zagnitko
Oct 11, 2008·Bioinformatics·Tim CarverMarie-Adèle Rajandream
Nov 7, 2009·Nucleic Acids Research·Tanja DavidsenGranger Sutton
Nov 11, 2009·Nucleic Acids Research·Luke E Ulrich, Igor B Zhulin
Dec 4, 2009·PloS One·Shannan J Ho SuiFiona S L Brinkman
Nov 30, 2010·Nucleic Acids Research·Sailu YellaboinaRaja Jothi
Nov 10, 2011·Nucleic Acids Research·Karen YookPaul W Sternberg
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Dec 24, 2011·Nucleic Acids Research·Victor M MarkowitzNikos C Kyrpides

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Citations

Dec 4, 2012·Nucleic Acids Research·Matthew D WhitesideFiona S L Brinkman
May 17, 2013·Nucleic Acids Research·Bhavjinder K DhillonFiona S L Brinkman
Mar 14, 2013·Journal of Chemical Ecology·Jennifer Sorensen ForbeyWilliam J Foley
Apr 24, 2013·Ecology and Evolution·Timothée PoisotDominique Gravel
Oct 7, 2015·Frontiers in Bioengineering and Biotechnology·Sarah E SchmedesBruce Budowle
Apr 29, 2015·Nucleic Acids Research·Bhavjinder K DhillonFiona S L Brinkman
Jun 16, 2018·Bioinformatics·Claire Bertelli, Fiona S L Brinkman
May 5, 2017·Nucleic Acids Research·Claire BertelliFiona Sl Brinkman

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Software Mentioned

MicrobeDB
GMOD
BioSQL
MicrobeDB Perl API
RAST
Aspera
Fasta
GBrowse
MicrobeDB Perl
Perl API

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