Bioinformatics Vol. 16 no. 11 2000
Pages 1046-1047
© 2000 Oxford University Press
Applications Note |
VISTA : visualizing global DNA sequence alignments of arbitrary length
1 National Energy Research Scientific
Computing Center
2 Genome Sciences Department, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
3 Department of Mathematics University of
California at Berkeley, Berkeley, CA 94720, USA
Received on June 1, 2000
; revised on July 19, 2000
; accepted on August 2, 2000
Summary: VISTA is a program for visualizing global DNA sequence alignments of arbitrary length. It has a clean output, allowing for easy identification of similarity, and is easily configurable, enabling the visualization of alignments of various lengths at different levels of resolution. It is currently available on the web, thus allowing for easy access by all researchers.
Availability: VISTA server is available on the web at http://www-gsd.lbl.gov/vista. The source code is available upon request.
Contact: vista{at}lbl.gov
To whom correspondence should be addressed.
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|
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|
|
|
|
|
|
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|
|
|
|
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|
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|
|
|
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|
|
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|
|
|
|
 |
|
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|
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|
|
|
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V. Valverde-Garduno, B. Guyot, E. Anguita, I. Hamlett, C. Porcher, and P. Vyas Differences in the chromatin structure and cis-element organization of the human and mouse GATA1 loci: implications for cis-element identification Blood, November 15, 2004; 104(10): 3106 - 3116. [Abstract] [Full Text] [PDF]
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S.-H. Im, A. Hueber, S. Monticelli, K.-H. Kang, and A. Rao Chromatin-level Regulation of the IL10 Gene in T Cells J. Biol. Chem., November 5, 2004; 279(45): 46818 - 46825. [Abstract] [Full Text] [PDF]
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E. Dodou, M. P. Verzi, J. P. Anderson, S.-M. Xu, and B. L. Black Mef2c is a direct transcriptional target of ISL1 and GATA factors in the anterior heart field during mouse embryonic development Development, August 15, 2004; 131(16): 3931 - 3942. [Abstract] [Full Text] [PDF]
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S. Pal, M. J. Nemeth, D. Bodine, J. L. Miller, J. Svaren, S. L. Thein, P. J. Lowry, and E. H. Bresnick Neurokinin-B Transcription in Erythroid Cells: DIRECT ACTIVATION BY THE HEMATOPOIETIC TRANSCRIPTION FACTOR GATA-1 J. Biol. Chem., July 23, 2004; 279(30): 31348 - 31356. [Abstract] [Full Text] [PDF]
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D. Kurokawa, N. Takasaki, H. Kiyonari, R. Nakayama, C. Kimura-Yoshida, I. Matsuo, and S. Aizawa Regulation of Otx2 expression and its functions in mouse epiblast and anterior neuroectoderm Development, July 15, 2004; 131(14): 3307 - 3317. [Abstract] [Full Text] [PDF]
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 C. J. Hatcher, N. Y.S.-G. Diman, M.-S. Kim, D. Pennisi, Y. Song, M. M. Goldstein, T. Mikawa, and C. T. Basson A role for Tbx5 in proepicardial cell migration during cardiogenesis Physiol Genomics, July 8, 2004; 18(2): 129 - 140. [Abstract] [Full Text] [PDF]
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A. Palsson, A. Rouse, R. Riley-Berger, I. Dworkin, and G. Gibson Nucleotide Variation in the Egfr Locus of Drosophila melanogaster Genetics, July 1, 2004; 167(3): 1199 - 1212. [Abstract] [Full Text] [PDF]
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K. A. Frazer, L. Pachter, A. Poliakov, E. M. Rubin, and I. Dubchak VISTA: computational tools for comparative genomics Nucleic Acids Res., July 1, 2004; 32(suppl_2): W273 - W279. [Abstract] [Full Text] [PDF]
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I. Ovcharenko, M. A. Nobrega, G. G. Loots, and L. Stubbs ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes Nucleic Acids Res., July 1, 2004; 32(suppl_2): W280 - W286. [Abstract] [Full Text] [PDF]
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 A. Zuniga, O. Michos, F. Spitz, A.-P. G. Haramis, L. Panman, A. Galli, K. Vintersten, C. Klasen, W. Mansfield, S. Kuc, et al. Mouse limb deformity mutations disrupt a global control region within the large regulatory landscape required for Gremlin expression Genes & Dev., July 1, 2004; 18(13): 1553 - 1564. [Abstract] [Full Text] [PDF]
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M. P. Hardy and L. A. J. O'Neill The Murine Irak2 Gene Encodes Four Alternatively Spliced Isoforms, Two of Which Are Inhibitory J. Biol. Chem., June 25, 2004; 279(26): 27699 - 27708. [Abstract] [Full Text] [PDF]
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I. Ovcharenko, D. Boffelli, and G. G. Loots eShadow: A Tool for Comparing Closely Related Sequences Genome Res., June 1, 2004; 14(6): 1191 - 1198. [Abstract] [Full Text] [PDF]
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B. T. MacDonald, M. Adamska, and M. H. Meisler Hypomorphic expression of Dkk1 in the doubleridge mouse: dose dependence and compensatory interactions with Lrp6 Development, June 1, 2004; 131(11): 2543 - 2552. [Abstract] [Full Text] [PDF]
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S. B. Montgomery, T. Astakhova, M. Bilenky, E. Birney, T. Fu, M. Hassel, C. Melsopp, M. Rak, A. G. Robertson, M. Sleumer, et al. Sockeye: A 3D Environment for Comparative Genomics Genome Res., May 1, 2004; 14(5): 956 - 962. [Abstract] [Full Text] [PDF]
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 Y. Wang, B. Jones Voy, S. Urs, S. Kim, M. Soltani-Bejnood, N. Quigley, Y.-R. Heo, M. Standridge, B. Andersen, M. Dhar, et al. The Human Fatty Acid Synthase Gene and De Novo Lipogenesis Are Coordinately Regulated in Human Adipose Tissue J. Nutr., May 1, 2004; 134(5): 1032 - 1038. [Abstract] [Full Text] [PDF]
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B. Hou, M. Eren, C. A. Painter, J. W. Covington, J. D. Dixon, J. A. Schoenhard, and D. E. Vaughan Tumor Necrosis Factor {alpha} Activates the Human Plasminogen Activator Inhibitor-1 Gene through a Distal Nuclear Factor {kappa}B Site J. Biol. Chem., April 30, 2004; 279(18): 18127 - 18136. [Abstract] [Full Text] [PDF]
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 T. J. Nelson, S. A. Duncan, and R. P. Misra Conserved Enhancer in the Serum Response Factor Promoter Controls Expression During Early Coronary Vasculogenesis Circ. Res., April 30, 2004; 94(8): 1059 - 1066. [Abstract] [Full Text] [PDF]
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K. L. Abrams, J. Xu, C. Nativelle-Serpentini, S. Dabirshahsahebi, and M. B. Rogers An Evolutionary and Molecular Analysis of Bmp2 Expression J. Biol. Chem., April 16, 2004; 279(16): 15916 - 15928. [Abstract] [Full Text] [PDF]
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B. Sevetson, S. Taylor, and Y. Pan Cbfa1/RUNX2 Directs Specific Expression of the Sclerosteosis Gene (SOST) J. Biol. Chem., April 2, 2004; 279(14): 13849 - 13858. [Abstract] [Full Text] [PDF]
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M. Brudno, A. Poliakov, A. Salamov, G. M. Cooper, A. Sidow, E. M. Rubin, V. Solovyev, S. Batzoglou, and I. Dubchak Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human Genome Res., April 1, 2004; 14(4): 685 - 692. [Abstract] [Full Text] [PDF]
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I. Ovcharenko, G. G. Loots, R. C. Hardison, W. Miller, and L. Stubbs zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles Genome Res., March 1, 2004; 14(3): 472 - 477. [Abstract] [Full Text] [PDF]
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D. U. Lee, O. Avni, L. Chen, and A. Rao A Distal Enhancer in the Interferon-{gamma} (IFN-{gamma}) Locus Revealed by Genome Sequence Comparison J. Biol. Chem., February 6, 2004; 279(6): 4802 - 4810. [Abstract] [Full Text] [PDF]
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I. A. Barash, L. Mathew, A. F. Ryan, J. Chen, and R. L. Lieber Rapid muscle-specific gene expression changes after a single bout of eccentric contractions in the mouse Am J Physiol Cell Physiol, February 1, 2004; 286(2): C355 - C364. [Abstract] [Full Text]
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R. M. Clark, E. Linton, J. Messing, and J. F. Doebley Inaugural Article: Pattern of diversity in the genomic region near the maize domestication gene tb1 PNAS, January 20, 2004; 101(3): 700 - 707. [Abstract] [Full Text] [PDF]
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P. Castronuevo, M. A. Thornton, L. E. McCarthy, J. Klimas, and B. P. Schick DNase I Hypersensitivity Patterns of the Serglycin Proteoglycan Gene in Resting and Phorbol 12-Myristate 13-Acetate-stimulated Human Erythroleukemia (HEL), CHRF 288-11, and HL-60 Cells Compared with Neutrophils and Human Umbilical Vein Endothelial Cells J. Biol. Chem., December 5, 2003; 278(49): 48704 - 48712. [Abstract] [Full Text] [PDF]
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