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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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.
Mount, D. W. (2001) Bioinformatics Sequence and Genome Analysis. Cold Spring Harbour Laboratory Press, Cold Spring Harbour, New York.
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.
Smith, T. F. and Waterman, M. S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197.
Huang, W., Umbach, D. M., and Leping, L. (2006) Accurate anchoring alignment of divergent sequences. Bioinformatics 22,29–34.
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.
Korf, I., Yandell, M., and Bedell, J. (2003) BLAST. O’Reilly and Associates, Sebastopol, CA.
Kurtz, S., Phillippy, A., Delcher, A. L., et al. (2004) Versatile and open software for comparing large genomes. Genome Biol. 5, R12.
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.
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.
Schwartz, S., Kent, W. J., Smit, A., et al. (2003) Human-mouse alignments with BLASTZ. Gen. Res. 13, 103–107.
Zhang, Z., Berman, P., Wiehe, T., and Miller, W. (1999) Post-processing long pairwise alignments. Bioinformatics 15, 1012–1019.
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.
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.
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, 3665–3666
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.
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.
Acknowledgments
This work was supported by the Faculties of Life Sciences and Medicine, Imperial College London and the Wellcome Trust.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc.
About this protocol
Cite this protocol
Abbott, J.C., Aanensen, D.M., Bentley, S.D. (2007). WebACT. In: Bergman, N.H. (eds) Comparative Genomics. Methods in Molecular Biology™, vol 395. Humana Press. https://doi.org/10.1007/978-1-59745-514-5_4
Download citation
DOI: https://doi.org/10.1007/978-1-59745-514-5_4
Publisher Name: Humana Press
Print ISBN: 978-1-58829-693-1
Online ISBN: 978-1-59745-514-5
eBook Packages: Springer Protocols