BASys: a web server for automated bacterial genome annotation
- Gary Van Domselaar
- Paul Stothard, Department of Agricultural, Food and Nutritional Science (AFNS)
- Savita Shrivastava
- Joseph Cruz
- An Chi Guo
- Xiaoli Dong
- Paul Lu, Department of Computing Science
- Duane Szafron, UofA CS
- Russ Greiner, Dept of Computing Science; PI of AICML
- David S. Wishart, Departments of Computing Science and Biology, University of Alberta
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.
Citation
G. Van Domselaar, P. Stothard, S. Shrivastava, J. Cruz, A. Guo, X. Dong, P. Lu, D. Szafron, R. Greiner, D. Wishart. "BASys: a web server for automated bacterial genome annotation". Nucleic Acids Research (NAR), 33((Web Server issue)), pp W455-W459, July 2005.| Keywords: | bioinformatics, genome, annotation, machine learning, medical informatics |
| Category: | In Journal |
| Web Links: | NAR Webpage |
BibTeX
@article{VanDomselaar+al:NAR05,
author = {Gary Van Domselaar and Paul Stothard and Savita Shrivastava and
Joseph Cruz and An Chi Guo and Xiaoli Dong and Paul Lu and Duane Szafron
and Russ Greiner and David S. Wishart},
title = {BASys: a web server for automated bacterial genome annotation},
Volume = "33",
Number = {(Web Server issue)},
Pages = {W455-W459},
journal = {Nucleic Acids Research (NAR)},
year = 2005,
}Last Updated: April 27, 2012Submitted by Russ Greiner
