Markowitz, V. M. et al. IMG: the integrated microbial genomes database and comparative analysis system.
There are a number of databases, including, for instance, the microbial genome database for comparative analysis (29 31) and the integrated microbial genomes (32 35) system, which provide a wide array of microbial genomes including some Fusobacterium strains for comparative genomics.
Microbial Genome Database for Comparative Analysis (MBGD) [ 28] and the Integrated Microbial Genomes (IMG) system [ 29] do provide a wide array of microbial genomes including some Helicobacter strains for comparative genomics, but lack the virulence factor perspective for comparative pathogenomics.
The protein sequences of microbial genomes were downloaded from the Microbial Genome Database (archive no. mbgd_2011-01).
MCT analyzed microbial genome databases.
Many types of microbial genome databases exist.
Homology searching by BLAST [ 75] was carried out against the following databases: NCBI [ 76] DFCI Grape Gene Index [ 77], Genoscope Grape Genome database [ 78], UNIPROT [ 79], PFGD Phytophthora Functional Genomics Database [ 80] and VBI Microbial Database [ 81].
Sequences from cellular microbes were identified using Real Time Genomics Map and Species programs, version 3.4.3 (Real Time Genomics, Hamilton, New Zealand, http://realtimegenomics.com) to align sequences against the Human Microbiome Project's microbial reference genome database (http://hmpdacc.org/HMREFG/), and by classifying sequences with MetaPhlAn [ 11].
In 2005, with the massive increase of DNA sequence data, the maintenance of the software system ARB and the corresponding rRNA databases SILVA was split between Munich and the Microbial Genomics and Bioinformatics Research Group in Bremen.
The Department of Energy DOE Office ofof Biological and Environmental Research funded genomics research in the Life Sciences funding category under the subcategories of Microbial Genomics, Genomics: GTL [Genomes To Life program], Human Genome, and Functional Genomics/Health Effects [ 33- 36].
Microbial genomics 3 (2017).
