Abstract
Comparative analysis of DNA sequences is becoming one of the major methods for discovery of functionally important genomic intervals. Presented here the VISTA family of computational tools was built to help researchers in this undertaking. These tools allow the researcher to align DNA sequences, quickly visualize conservation levels between them, identify highly conserved regions, and analyze sequences of interest through one of the following approaches:
-
• Browse precomputed whole-genome alignments of vertebrates and other groups of organisms.
-
• Submit sequences to GenomeVISTA to align them to whole genomes.
-
• Submit two or more sequences to mVISTA to align them with each other (a variety of alignment programs with several distinct capabilities are made available).
-
• Submit sequences to Regulatory VISTA (rVISTA) to perform transcription factor binding site predictions based on conservation within sequence alignments.
-
• Use stand-alone alignment and visualization programs to run comparative sequence analysis locally.
All VISTA tools use standard algorithms for visualization and conservation analysis to make comparison of results from different programs more straightforward. The web page http://genome.lbl.gov/vista/ serves as a portal for access to all VISTA tools. Our support group can be reached by email at vista@lbl.gov.
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
Batzoglou, S., Pachter, L., Mesirov, J. P., Berger, B., and Lander E. S. (2000) Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res. 10, 950–958.
Brent, M. R. and Guigo, R. (2004) Recent advances in gene structure prediction.Curr. Opin. Struct. Biol. 14, 264–272.
Guigo, R., Dermitzakis, E. T., Agarwal, P., et al. (2003) Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc. Natl. Acad. Sci. USA 100, 1140–1145.
Pennacchio, L. A., Olivier, M., Hubacek, J. A., et al. (2001) An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing.Science 294, 169–173.
Woolfe, A., Goodson, M., Goode, D. K., et al. (2004) Highly conserved noncoding sequences are associated with vertebrate development. PLoS Biol. 3, e7.
Gottgens, B., Barton, L. M., Chapman, M. A., et al. (2002) Transcriptional regulation of the stem cell leukemia gene (SCL)—comparative analysis of five vertebrate SCL loci. Genome Res. 12, 749–759.
Waterston, R. H., Lindblad-Toh, K., Birney, E., et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562.
Gibbs, R. A., Weinstock, G. M., Metzker, M. L., et al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428,493–521.
Kirkness, E. F., Bafna, V., Halpern, A. L., et al. (2003) The dog genome: survey sequencing and comparative analysis. Science 301, 1898–1903.
Hillier, L. W., Miller, W., Birney, E., et al. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.Nature 432, 695–716.
Hardison, R. C. (2003) Comparative genomics. PLoS Biol. 1, 156–160.
Miller, W., Makova, K. D., Nekrutenko, A., and Hardison, R. C. (2004) Comparative genomics. Annu. Rev. Genom. Hum. Genet. 5, 15–56.
Dubchak, I. and Frazer, K. (2003) Multi-species sequence comparison: the next frontier in genome annotation. Genome Biol. 4, 122–128.
Frazer, K. A, Elnitski, L., Church, D. M., Dubchak, I., and Hardison, R. C. (2003) Cross-species sequence comparisons: a review of methods and available resources.Genome Res. 13, 1–12.
Wei, L., Liu, I., Dubchak, I., Shon, J., and Park J. (2002) Comparative genomics approaches to study organism similarities and differences. J. Biomed. Inform. 35,142–150.
Frazer, K. A., Pachter, L., Poliakov, A., Rubin E. M., and Dubchak, I. (2004) VISTA—computational tools for comparative genomics. Nucleic Acids. Res. 32(Web Server issue):W273.
Dubchak, I., Brudno, M., Pachter, L. S., et al. (2000) Active conservation of noncoding sequences revealed by 3-way species comparisons. Genome Res. 10, 1304–1306.
Mayor, C., Brudno, M., Schwartz, J. R., et al. (2000) VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16, 1046–1047.
Loots, G., Ovcharenko, I., Pachter, L., Dubchak, I., and Rubin E. (2002) rVISTA for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res. 12, 832–839.
Bray, N., Dubchak, I., and Pachter, L. (2003) AVID: a global alignment program. Genome Res. 13, 97–102.
Brudno, M., Do, C. B., Cooper, G. M., et al., and NISC Comparative Sequencing Program (2003) LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13, 721–731.
Couronne, O., Poliakov, A., Bray, N., et al. (2003) Strategies and tools for whole genome alignments. Genome Res. 13, 73–80.
Brudno, M., Poliakov, A., Salamov, A., et al. (2004) Automated whole-genome multiple alignment of rat, mouse, and human. Genome Res. 14, 685–692.
Schwartz, S., Zhang, Z., Frazer, K. A., et al. (2000) PipMaker—a web server for aligning two genomic DNA sequences. Genome Res. 10, 577–586.
Schwartz, S., Elnitski, L., Li, M., et al., and NISC Comparative Sequencing Program (2003) MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res. 31, 3518–3524.
Schwartz, S., Kent, W. J., Smit, A., et al. (2003) Human-mouse alignments with BLASTZ. Genome Res. 13, 103–107.
Pollard, D. A., Bergman, C. M, Stoye, J., Celniker, S. E., and Eisen, M. B. (2004) Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 5, 6–22.
van der Helm-van Mil, A. H., Wesoly, J. Z., and Huizinga, T. W. (2005) Understanding the genetic contribution to rheumatoid arthritis. Curr. Opin. Rheumatol. 17, 299–304.
Yamada, R. and Ymamoto, K. (2005) Recent findings on genes associated with inflammatory disease. Mutat. Res. 573, 136–151.
Brudno, M., Malde, S., Poliakov, A., et al. (2003) Glocal alignment: finding rearrangements during alignment. Bioinformatics Suppl 1, 154–162.
Shah, N., Couronne, O., Pennacchio, L. A., et al. (2004) Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics 20, 636–643.
Martin, J., Han, C., Gordon, L. A., et al. (2004) The sequence and analysis of duplication-rich human chromosome 16. Nature 432, 988–994.
Parent, S. A., Zhang, T., Chrebet, G., et al. (2002) Molecular characterization of the murine SIGNR1 gene encoding a C-type lectin homologous to human DC-SIGN and DC-SIGNR. Gene 293, 33–46.
Chen, J., Kitchen, C. M., Streb, J. W., and Miano, J. (2002) Myocardin: a component of a molecular switch for smooth muscle differentiation. J. Mol. Cell. Cardiol. 34, 1345–1356.
Premzl, M., Delbridge, M., Gready, J. E., et al. (2005) The prion protein gene:identifying regulatory signals using marsupial sequence. Gene 349C, 121–134.
Anguita, E., Sharpe, J. A., Sloane-Stanley, J. A., Tufarelli, C., Higgs, D. R., and Wood W. G. (2002) Deletion of the mouse a-globin regulatory element (HS 26) has an unexpectedly mild phenotype. Blood 100, 3450–3456.
Cooper, G. M., Brudno, M., Stone, E. A, Dubchak, I., Batzoglou, S., and Sidow, A.(2004) Characterization of evolutionary rates and constraints in three mammalian genomes. Genome Res. 14, 539–548.
Margulies, E. H., Vinson, J. P., Miller, W., et al. (2005) An initial strategy for the systematic identification of functional elements in the human genome by lowredundancy comparative sequencing. Proc. Natl. Acad. Sci. USA 102, 4795–4800.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Humana Press Inc.
About this protocol
Cite this protocol
Dubchak, I., Ryaboy, D.V. (2006). VISTA Family of Computational Tools for Comparative Analysis of DNA Sequences and Whole Genomes. In: Bina, M. (eds) Gene Mapping, Discovery, and Expression. Methods in Molecular Biology, vol 338. Humana Press. https://doi.org/10.1385/1-59745-097-9:69
Download citation
DOI: https://doi.org/10.1385/1-59745-097-9:69
Publisher Name: Humana Press
Print ISBN: 978-1-58829-575-0
Online ISBN: 978-1-59745-097-3
eBook Packages: Springer Protocols