VISTA: computational tools for comparative genomics
Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, CA 94043, USA, 1 Department of Mathematics, University of California—Berkeley, Berkeley, CA, 94720, USA, 2 Genomics Division, Lawrence Berkeley National Laboratory, MS 84-171, Berkeley, CA 94720, USA and 3 Department of Energy Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA 94598, USA
* To whom correspondence should be addressed. Tel: +1 510 495 2419; Fax: +1 510 486 5614; Email: ildubchak{at}lbl.gov
Received February 16, 2004; Revised and Accepted April 26, 2004
Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/vista/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, to submit their own sequences of interest to several VISTA servers for various types of comparative analysis and to obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein.
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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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|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
D. Swarbreck, C. Wilks, P. Lamesch, T. Z. Berardini, M. Garcia-Hernandez, H. Foerster, D. Li, T. Meyer, R. Muller, L. Ploetz, et al. The Arabidopsis Information Resource (TAIR): gene structure and function annotation Nucleic Acids Res., January 11, 2008; 36(suppl_1): D1009 - D1014. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
B. Palenik, J. Grimwood, A. Aerts, P. Rouze, A. Salamov, N. Putnam, C. Dupont, R. Jorgensen, E. Derelle, S. Rombauts, et al. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation PNAS, May 1, 2007; 104(18): 7705 - 7710. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Fremez, T. Faraut, G. Fichant, J. Gouzy, and Y. Quentin Phylogenetic exploration of bacterial genomic rearrangements Bioinformatics, May 1, 2007; 23(9): 1172 - 1174. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. M. Alfieri, H. J. Evans-Anderson, and K. E. Yutzey Developmental regulation of the mouse IGF-I exon 1 promoter region by calcineurin activation of NFAT in skeletal muscle Am J Physiol Cell Physiol, May 1, 2007; 292(5): C1887 - C1894. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Fortschegger, B. Wagner, R. Voglauer, H. Katinger, M. Sibilia, and J. Grillari Early Embryonic Lethality of Mice Lacking the Essential Protein SNEV Mol. Cell. Biol., April 15, 2007; 27(8): 3123 - 3130. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Sosinsky, B. Honig, R. S. Mann, and A. Califano Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting PNAS, April 10, 2007; 104(15): 6305 - 6310. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Fuchs, C. Nilsson, J. Kachergus, M. Munz, E.-M Larsson, B. Schule, J. W. Langston, F. A. Middleton, O. A. Ross, M. Hulihan, et al. Phenotypic variation in a large Swedish pedigree due to SNCA duplication and triplication Neurology, March 20, 2007; 68(12): 916 - 922. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. M. Knosp, C. Saneyoshi, S. Shou, H. P. Bachinger, and H. S. Stadler Elucidation, Quantitative Refinement, and in Vivo Utilization of the HOXA13 DNA Binding Site J. Biol. Chem., March 2, 2007; 282(9): 6843 - 6853. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. J. Lugus, Y. S. Chung, J. C. Mills, S.-I. Kim, J. A. Grass, M. Kyba, J. M. Doherty, E. H. Bresnick, and K. Choi GATA2 functions at multiple steps in hemangioblast development and differentiation Development, January 15, 2007; 134(2): 393 - 405. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Visel, S. Minovitsky, I. Dubchak, and L. A. Pennacchio VISTA Enhancer Browser--a database of tissue-specific human enhancers Nucleic Acids Res., January 12, 2007; 35(suppl_1): D88 - D92. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. E. Kazakov, M. J. Cipriano, P. S. Novichkov, S. Minovitsky, D. V. Vinogradov, A. Arkin, A. A. Mironov, M. S. Gelfand, and I. Dubchak RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes Nucleic Acids Res., January 12, 2007; 35(suppl_1): D407 - D412. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Pachkov, I. Erb, N. Molina, and E. van Nimwegen SwissRegulon: a database of genome-wide annotations of regulatory sites Nucleic Acids Res., January 12, 2007; 35(suppl_1): D127 - D131. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T.-y. Roh, G. Wei, C. M. Farrell, and K. Zhao Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns Genome Res., January 1, 2007; 17(1): 74 - 81. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. A. Schlueter, I. F. Vasylenko-Sanders, S. Deshpande, J. Yi, M. Siegfried, B. A. Roe, S. D. Schlueter, B. E. Scheffler, and R. C. Shoemaker The FAD2 Gene Family of Soybean:: Insights into the Structural and Functional Divergence of a Paleopolyploid Genome Crop Sci., January 1, 2007; 47(Supplement_1): S-14 - S-26. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Ribich, B. Tasic, and T. Maniatis Identification of long-range regulatory elements in the protocadherin-{alpha} gene cluster PNAS, December 26, 2006; 103(52): 19719 - 19724. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Elnitski, V. X. Jin, P. J. Farnham, and S. J.M. Jones Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques Genome Res., December 1, 2006; 16(12): 1455 - 1464. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y.-f. Guo, D.-h. Xiong, H. Shen, L.-j. Zhao, P. Xiao, Y. Guo, W. Wang, T.-l. Yang, R. R Recker, and H.-w. Deng Polymorphisms of the low-density lipoprotein receptor-related protein 5 (LRP5) gene are associated with obesity phenotypes in a large family-based association study J. Med. Genet., October 1, 2006; 43(10): 798 - 803. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. A. Schlueter, B. E. Scheffler, S. D. Schlueter, and R. C. Shoemaker Sequence Conservation of Homeologous Bacterial Artificial Chromosomes and Transcription of Homeologous Genes in Soybean (Glycine max L. Merr.) Genetics, October 1, 2006; 174(2): 1017 - 1028. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Wang, Y. Su, A. J. Mackey, E. T. Kraemer, and J. C. Kissinger SynView: a GBrowse-compatible approach to visualizing comparative genome data Bioinformatics, September 15, 2006; 22(18): 2308 - 2309. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. GuhaThakurta Computational identification of transcriptional regulatory elements in DNA sequence Nucleic Acids Res., July 19, 2006; 34(12): 3585 - 3598. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. F. Mulley, C.-h. Chiu, and P. W. H. Holland Breakup of a homeobox cluster after genome duplication in teleosts PNAS, July 5, 2006; 103(27): 10369 - 10372. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Prabhakar, F. Poulin, M. Shoukry, V. Afzal, E. M. Rubin, O. Couronne, and L. A. Pennacchio Close sequence comparisons are sufficient to identify human cis-regulatory elements Genome Res., July 1, 2006; 16(7): 855 - 863. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. A. Gauthier and R. S. Hewes Transcriptional regulation of neuropeptide and peptide hormone expression by the Drosophila dimmed and cryptocephal genes J. Exp. Biol., May 15, 2006; 209(10): 1803 - 1815. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. R. t. Bosch, J. A. Benavides, and T. W. Cline The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription Development, May 15, 2006; 133(10): 1967 - 1977. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. P. Lee, E. G. L. Koh, A. Tay, S. Brenner, and B. Venkatesh Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters PNAS, May 2, 2006; 103(18): 6994 - 6999. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Patalano, G. Pruliere, F. Prodon, A. Paix, P. Dru, C. Sardet, and J. Chenevert The aPKC-PAR-6-PAR-3 cell polarity complex localizes to the centrosome attracting body, a macroscopic cortical structure responsible for asymmetric divisions in the early ascidian embryo J. Cell Sci., April 15, 2006; 119(8): 1592 - 1603. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Fisher, E. A. Grice, R. M. Vinton, S. L. Bessling, and A. S. McCallion Conservation of RET Regulatory Function from Human to Zebrafish Without Sequence Similarity Science, April 14, 2006; 312(5771): 276 - 279. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Chomette, M. Frain, S. Cereghini, P. Charnay, and J. Ghislain Krox20 hindbrain cis-regulatory landscape: interplay between multiple long-range initiation and autoregulatory elements Development, April 1, 2006; 133(7): 1253 - 1262. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
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|
|
|
|
 |
|
 A. Csiszar, M. Ahmad, K. E. Smith, N. Labinskyy, Q. Gao, G. Kaley, J. G. Edwards, M. S. Wolin, and Z. Ungvari Bone Morphogenetic Protein-2 Induces Proinflammatory Endothelial Phenotype Am. J. Pathol., February 1, 2006; 168(2): 629 - 638. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Feng, C. L. Sansam, M. Singh, and R. B. Emeson Altered RNA Editing in Mice Lacking ADAR2 Autoregulation Mol. Cell. Biol., January 15, 2006; 26(2): 480 - 488. [Abstract] [Full Text] [PDF]
|
|
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|
|
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T. Tran, P. Havlak, and J. Miller MicroRNA enrichment among short 'ultraconserved' sequences in insects. Nucleic Acids Res., January 1, 2006; 34(9): e65 - e65. [Abstract] [Full Text] [PDF]
|
|
|
|
|
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S. A. Shabalina, A. Y. Ogurtsov, and N. A. Spiridonov A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res., January 1, 2006; 34(8): 2428 - 2437. [Abstract] [Full Text] [PDF]
|
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V. M. Markowitz, F. Korzeniewski, K. Palaniappan, E. Szeto, G. Werner, A. Padki, X. Zhao, I. Dubchak, P. Hugenholtz, I. Anderson, et al. The integrated microbial genomes (IMG) system Nucleic Acids Res., January 1, 2006; 34(suppl_1): D344 - D348. [Abstract] [Full Text] [PDF]
|
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N. Sierro, T. Kusakabe, K.-J. Park, R. Yamashita, K. Kinoshita, and K. Nakai DBTGR: a database of tunicate promoters and their regulatory elements Nucleic Acids Res., January 1, 2006; 34(suppl_1): D552 - D555. [Abstract] [Full Text] [PDF]
|
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E. A. Grice, E. S. Rochelle, E. D. Green, A. Chakravarti, and A. S. McCallion Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer Hum. Mol. Genet., December 15, 2005; 14(24): 3837 - 3845. [Abstract] [Full Text] [PDF]
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J. Lazar, C. Moreno, H. J. Jacob, and A. E. Kwitek Impact of genomics on research in the rat Genome Res., December 1, 2005; 15(12): 1717 - 1728. [Abstract] [Full Text] [PDF]
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S. N. Twigger, D. Pasko, J. Nie, M. Shimoyama, S. Bromberg, D. Campbell, J. Chen, N. d. Cruz, C. Fan, C. Foote, et al. Tools and strategies for physiological genomics: the Rat Genome Database Physiol Genomics, October 17, 2005; 23(2): 246 - 256. [Abstract] [Full Text] [PDF]
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E. de la Calle-Mustienes, C. G. Feijoo, M. Manzanares, J. J. Tena, E. Rodriguez-Seguel, A. Letizia, M. L. Allende, and J. L. Gomez-Skarmeta A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts Genome Res., August 1, 2005; 15(8): 1061 - 1072. [Abstract] [Full Text] [PDF]
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M. G. Schueler, J. M. Dunn, C. P. Bird, M. T. Ross, L. Viggiano, NISC Comparative Sequencing Program, M. Rocchi, H. F. Willard, and E. D. Green Progressive proximal expansion of the primate X chromosome centromere PNAS, July 26, 2005; 102(30): 10563 - 10568. [Abstract] [Full Text] [PDF]
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S. Roepcke, P. Fiziev, P. H. Seeburg, and M. Vingron SVC: structured visualization of evolutionary sequence conservation Nucleic Acids Res., July 1, 2005; 33(suppl_2): W271 - W273. [Abstract] [Full Text] [PDF]
|
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|
|
|
K. S. Pappu, E. J. Ostrin, B. W. Middlebrooks, B. T. Sili, R. Chen, M. R. Atkins, R. Gibbs, and G. Mardon Dual regulation and redundant function of two eye-specific enhancers of the Drosophila retinal determination gene dachshund Development, June 15, 2005; 132(12): 2895 - 2905. [Abstract] [Full Text] [PDF]
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 |
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 A. Csiszar, K. E. Smith, A. Koller, G. Kaley, J. G. Edwards, and Z. Ungvari Regulation of Bone Morphogenetic Protein-2 Expression in Endothelial Cells: Role of Nuclear Factor-{kappa}B Activation by Tumor Necrosis Factor-{alpha}, H2O2, and High Intravascular Pressure Circulation, May 10, 2005; 111(18): 2364 - 2372. [Abstract] [Full Text] [PDF]
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D. A. Hutcheson, M. I. Hanson, K. B. Moore, T. T. Le, N. L. Brown, and M. L. Vetter bHLH-dependent and -independent modes of Ath5 gene regulation during retinal development Development, February 15, 2005; 132(4): 829 - 839. [Abstract] [Full Text] [PDF]
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