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)


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.


BLAST MUMmer BLASTZ genome comparison visualization database precomputed bacteria plasmid chromosome 



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


  1. 1.
    Kersey P., Bower, L., Morris, L., et al. (2005) Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res. 33, 297–302.CrossRefGoogle Scholar
  2. 2.
    Mount, D. W. (2001) Bioinformatics Sequence and Genome Analysis. Cold Spring Harbour Laboratory Press, Cold Spring Harbour, New York.Google Scholar
  3. 3.
    Needleman, S. B. and Wunsch, C. D. (1970) A general method applicable to the search for similarities in the amino-acid sequence of two proteins.J. Mol. Biol. 48, 443–453.CrossRefPubMedGoogle Scholar
  4. 4.
    Smith, T. F. and Waterman, M. S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197.CrossRefPubMedGoogle Scholar
  5. 5.
    Huang, W., Umbach, D. M., and Leping, L. (2006) Accurate anchoring alignment of divergent sequences. Bioinformatics 22,29–34.CrossRefPubMedGoogle Scholar
  6. 6.
    Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) “Basic local alignment tool. J. Mol. Biol. 215, 403–410.PubMedGoogle Scholar
  7. 7.
    Korf, I., Yandell, M., and Bedell, J. (2003) BLAST. O’Reilly and Associates, Sebastopol, CA.Google Scholar
  8. 8.
    Kurtz, S., Phillippy, A., Delcher, A. L., et al. (2004) Versatile and open software for comparing large genomes. Genome Biol. 5, R12.CrossRefPubMedGoogle Scholar
  9. 9.
    Chain. P., Kurtz, S., Ohlebusch, E., and Slezak, T. (2003) An applications-focused review of comparative genomics tools: capabilities, limitations and future challenges. Brief. Bioinform. 4, 105–123.CrossRefPubMedGoogle Scholar
  10. 10.
    Schwartz, S., Zhang, Z., Frazer, K. A., et al. (2000) PipMaker: a web server for aligning two genomic DNA sequences. Gen. Res. 10, 577–586.CrossRefGoogle Scholar
  11. 11.
    Schwartz, S., Kent, W. J., Smit, A., et al. (2003) Human-mouse alignments with BLASTZ. Gen. Res. 13, 103–107.CrossRefGoogle Scholar
  12. 12.
    Zhang, Z., Berman, P., Wiehe, T., and Miller, W. (1999) Post-processing long pairwise alignments. Bioinformatics 15, 1012–1019.CrossRefPubMedGoogle Scholar
  13. 13.
    Delcher, A. L., Kasif, S., Fleischmann, R. D., Peterson, J., White, O., and Salzberg, S. L. (1999) Alignment of whole genomes. Nuc. Acids. Res. 27, 2369–2376.CrossRefGoogle Scholar
  14. 14.
    Carver, T. J., Rutherford, K. M., Berriman, M., Rajandream, M. A., Barrell, B. G., and Parkhill, J. (2005) ACT: the Artemis Comparison Tool. Bioinformatics 21, 3422–3433.CrossRefPubMedGoogle Scholar
  15. 15.
    Abbott, J. C., Aanensen, D. M., Rutherford, K., Butcher, S., and Spratt, B. G. (2005) WebACT: an online companion for the Artemis Comparison Tool. Bioinformatics 21, 3665–3666CrossRefPubMedGoogle Scholar
  16. 16.
    Parkhill, J., Sebaihia, M., Preston, A., et al. (2003) Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat. Genet. 35, 32–40.CrossRefPubMedGoogle Scholar
  17. 17.
    Bentley, S. D., Aanensen, D. M., Mavroidi, A., et al. (2006) Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. PLoS Genet 2, e31.Google Scholar

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

Personalised recommendations