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. 2005 Jul 1;33(Web Server issue):W455-9.
doi: 10.1093/nar/gki593.

BASys: a web server for automated bacterial genome annotation

Gary H Van Domselaar  1 , Paul Stothard, Savita Shrivastava, Joseph A Cruz, AnChi Guo, Xiaoli Dong, Paul Lu, Duane Szafron, Russ Greiner, David S Wishart
Affiliations

BASys: a web server for automated bacterial genome annotation

Gary H Van Domselaar et al. Nucleic Acids Res. .

Abstract

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 approximately 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 approximately 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 http://wishart.biology.ualberta.ca/basys.

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Figures

Figure 1
Figure 1
A schematic outline of the BASys architecture. (A) The web server, hosted on the master node, accepts genome data and schedules it for processing by the slave nodes. (B) Each slave node hosts a BASys annotation engine. The annotation pipeline combines similarity searching and sequence analysis to generate annotations.
Figure 2
Figure 2
A screenshot montage of the BASys server showing the different kinds of graphical and textual output available. Shown are the annotation progress monitor for two genome annotation projects (E.coli and C.trachomatis) in various states of completion, a full-scale and expanded graphical genome map for E.coli and a sample annotation report.
See this image and copyright information in PMC

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