BASys: A web server for automated bacterial genome annotation

• Author(s) / Creator(s)

  • Stothard, P.
  • Lu, P.
  • Cruz, J.A.
  • Szafron, D.
  • Van Domselaar, G.H.
  • Shrivistava, S.
  • Guo, A.
  • Dong, X.
  • Grenier, R.
  • Wishart, D.S.

• 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.

• Date created

  2005

• Subjects / Keywords

  • Sequences
  • Databases
  • Protein families

• Type of Item

  Article (Published)

• DOI

  https://doi.org/10.7939/R31K35

• License

  © 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@oupjournals.org