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WebACT

An Online Genome Comparison Suite
  • James C. Abbott
  • David M. Aanensen
  • Stephen D. Bentley
Part of the Methods in Molecular Biology™ book series (MIMB, volume 395)

Summary

Comparison of related genomes is an enormously powerful technique for explaining phenotypic differences and revealing recent evolutionary events. Genomes evolve through a host of mechanisms including long- and short-range intragenomic rearrangements, insertion of laterally acquired DNA, gene loss, and single-nucleotide polymorphisms. The Artemis Comparison Tool (ACT) was developed to enable the intuitive visualization of the consequences of such events in the context of two or more aligned genomes. WebACT is an online resource designed to allow the alignment of up to five genomic sequences within the ACT environment without the need for local software installation. Comparisons can be carried out between uploaded sequences, or those selected from the EMBL or RefSeq databases, using BLASTZ, MUMmer, or Basic Local Alignment Search Tool (BLAST). Precomputed comparisons can be selected from a database covering all the completed bacterial chromosome and plasmid sequences in the Genome Reviews database (1). This allows the rapid visualization of regions of interest, without the need to handle the full genome sequences.

Here, we describe the process of using WebACT to prepare comparisons for visualization, and the selection of precomputed comparisons from the database. The use of ACT to view the selected comparison is then explored using examples from bacterial genomes.

Keywords

BLAST MUMmer BLASTZ genome comparison visualization database precomputed bacteria plasmid chromosome 

Notes

Acknowledgments

This work was supported by the Faculties of Life Sciences and Medicine, Imperial College London and the Wellcome Trust.

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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • James C. Abbott
    • 1
  • David M. Aanensen
    • 2
  • Stephen D. Bentley
    • 3
  1. 1.Centre for BioinformaticsImperial College London
  2. 2.Department of Infectious Disease EpidemiologyImperial College London
  3. 3.Wellcome Trust Sanger InstituteWellcome Trust Genome CampusUK

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