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Bioinformatics Advance Access published online on August 2, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti601
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received May 23, 2005
Revised July 27, 2005
Accepted July 27, 2005

Applications note

WebACT - an online companion for the Artemis Comparison Tool

J. C. Abbott 1*, D. M. Aanensen 2, K. Rutherford 3, S. Butcher 1, and B. G. Spratt 2

1 Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, UK
2 Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG
3 Pathogen Sequencing Unit, Sanger Institute, Cambridge, CB10 1SA, UK; Current Address: Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK

* To whom correspondence should be addressed.
J. C. Abbott, E-mail: admin{at}webact.org


  Abstract

Summary: WebACT is an online resource which enables the rapid provision of simultaneous BLAST comparisons between up to five genomic sequences in a format amenable for visualization with the well-known Artemis Comparison Tool (ACT). Comparisons can be generated on-the-fly using sequences directly retrieved via EMBL database queries, or by entering or uploading user sequences. Furthermore, pre-computed comparisons are available between all publicly available, completed prokaryotic genomes and plasmids currently contained within the Genome Reviews database (372 sequences, representing 175 different species). The system is designed to minimise the volume of downloaded data and maximise performance. Genome sequences, annotation and pre-computed comparisons are stored in a relational database allowing flexible querying based on user-defined sequence regions; from whole genome to a defined region flanking a specified gene. Comparison and sequence files, whether computed on-line or retrieved from the database of pre-computed genome comparisons, can be viewed online using ACT and are available for download.

Availability: Freely accessible from http://www.webact.org.

Supplementary Information: User guide and worked examples available at http://www.webact.org/WebACT/docs.


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