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. 2012 Jan;40(Database issue):D599-604.
doi: 10.1093/nar/gkr1105. Epub 2011 Dec 1.

BacMap: an up-to-date electronic atlas of annotated bacterial genomes

Joseph Cruz  1 , Yifeng Liu, Yongjie Liang, You Zhou, Michael Wilson, Jonathan J Dennis, Paul Stothard, Gary Van Domselaar, David S Wishart
Affiliations

BacMap: an up-to-date electronic atlas of annotated bacterial genomes

Joseph Cruz et al. Nucleic Acids Res. 2012 Jan.

Abstract

Originally released in 2005, BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains fully labeled, zoomable and searchable chromosome maps for essentially all sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. The latest release of BacMap (http://bacmap.wishartlab.com/) now contains data for more than 1700 bacterial species (~10× more than the 2005 release), corresponding to more than 2800 chromosome and plasmid maps. All bacterial genome maps are now supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap also contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images (when available). Improved data browsing and searching tools have also been added to allow more facile filtering, sorting and display of the chromosome maps and their contents.

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Figures

Figure 1.
Figure 1.
A screenshot montage of the BacMap database showing the different display, browsing and filtering tools.
See this image and copyright information in PMC

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References

    1. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995;269:496–512. - PubMed
    1. Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salzberg SL. The value of complete microbial genome sequencing (you get what you pay for) J. Bacteriol. 2002;184:6403–6405. - PMC - PubMed
    1. Nagarajan N, Pop M. Sequencing and genome assembly using next-generation technologies. Methods Mol. Biol. 2010;673:1–17. - PubMed
    1. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2011;39:D32–D37. - PMC - PubMed
    1. Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics. 2005;21:537–539. - PubMed

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