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Nucleic Acids Research 2005 33(Web Server Issue):W455-W459; doi:10.1093/nar/gki593
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

BASys: a web server for automated bacterial genome annotation

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

Departments of Biological Sciences and Computing Science, University of Alberta Edmonton, AB, T6G 2E8, Canada

*To whom correspondence should be addressed. Tel: +1 780 492 0383; Fax: +1 780 492 1071; Email: david.wishart{at}ualberta.ca

Received February 13, 2005. Revised April 14, 2005. Accepted May 6, 2005.

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


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