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BASys: A web server for automated bacterial genome annotation Open Access


Author or creator
van Domselaar, Gary H.
Stothard, Paul
Shrivastava, Savita
Cruz, Joseph A.
Guo, AnChi
Dong, Xaoli
Lu, Paul
Szafron, Duane
Greiner, Russ
Wishart, David S.
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Protein Families
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Journal Article (Published)
BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. It accepts raw DNA sequence data and an optional list of gene identification information and provides extensive textual annotation and hyperlinked image output. BASys uses >30 programs to determine ∼60 annotation subfields for each gene, including gene/protein name, GO function, COG function, possible paralogues and orthologues, molecular weight, isoelectric point, operon structure, subcellular localization, signal peptides, transmembrane regions, secondary structure, 3D structure, reactions and pathways. The depth and detail of a BASys annotation matches or exceeds that found in a standard SwissProt entry. BASys also generates colorful, clickable and fully zoomable maps of each query chromosome to permit rapid navigation and detailed visual analysis of all resulting gene annotations. The textual annotations and images that are provided by BASys can be generated in ∼24 h for an average bacterial chromosome (5 Mb). BASys annotations may be viewed and downloaded anonymously or through a password protected access system. The BASys server and databases can also be downloaded and run locally. BASys is accessible at

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© 2005 van Domselaar, G.H., Stothard, P., Shrivastava, S., Cruz, J.A., Guo, A., Dong, X., Lu, P., Szafron, D., Greiner, R., & Wishart, D.S. This version of this article is open access and can be downloaded and shared. The original author(s) and source must be cited.

Citation for previous publication
van Domselaar, Gary H., Stothard, Paul, Shrivastava, Savita, Cruz, Joseph A., Guo, AnChi, Dong, Xaoli, Lu, Paul, Szafron, Duane, Greiner, Russ, & Wishart, David S. (2005). BASys: A web server for automated bacterial genome annotation. Nucleic Acids Research, 33(Suppl. 2), W455-W459.


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