VISTA : visualizing global DNA sequence alignments of arbitrary length

By C. Mayor, Michael Brudno, J. R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior S. Pachter, Inna Dubchak. Bioinform., 2000

1,054 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/33a113ce3e317c57b06adc25eea9785e70603aac

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Citations in the corpus

VISTA: computational tools for comparative genomics (2004, background): “…(7) the user sub-mits a single sequence (draft or ﬁnished) which is compared with publicly available completed whole-genome assemblies. mVISTA (4,6) is the original program, designed for comparison of orthologous sequences of different species. rVISTA (9) combines a transcription factor…”
A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. (2003, methodology): “Comparison of this sequence to the mouse significantly reduced the overall similarity displayed by the VISTA plot and demonstrated a single conserved region of 800 bp corresponding to the 1.3 kb region predicted in human and mouse (Fig.”
Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects (2010, methodology): “Several universal tools have already been adopted in certain plastid comparative genomic studies, for example, REPuter (Kurtz et al., 2001) for dealing with SDRs, GRAPPA (http://www.cs.unm.edu/m̃oret/GRAPPA/) and GRIMM (Tesler, 2002) for genome rearrangements, as well as PipMaker (Schwartz et al., 2”
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement (2010, methodology): “browsers such as the UCSC browser [66], VISTA [67], and others”
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development (2004, positive): “The MLAGAN alignment was visualised using the VISTA program [76], enabling the identification of conserved sequences.”
Transcriptional regulation by calcium, calcineurin, and NFAT. (2003, background): “These regions often (but not always) correspond to highly conserved noncoding sequences (CNS) identified by comparing the sequences of gene loci in two or more mammalian genomes using Web-based programs such as VISTA (Mayor et al. 2000; Loots et al. 2002; Bray et al. 2003) or PipMaker (Schwartz et a”
Distribution and intensity of constraint in mammalian genomic sequence. (2005, background): “www.genome.org and characterization of constrained elements (Gumucio et al. 1992; Dubchak et al. 2000; Mayor et al. 2000; Sumiyama et al. 2001; Boffelli et al. 2003; Margulies et al. 2003; Cooper et al. 2004a; Shah et al. 2004; Siepel and Haussler 2004a) suffer from one, or multiple, of several…”
Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. (2002, methodology): “The two genes share the upstream intergenic DNA sequence of 450 nt. Comparisons of sequence similarities using the VISTA alignment tool ( Mayor et al. 2000; http://www-gsd.lbl.gov/vista) show the expected strong conservation of exon sequences and reduced similarity in noncoding regions (Fig. 3B), a”
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes (2004, methodology): “The conservation-profile visualization scheme of the ECR Browser tool is based on an idea originally implemented in the PipMaker tool (21) and later adopted by both Vista (22) and zPicture (23).”
PharmGKB: the Pharmacogenetics Knowledge Base (2002, background): “For researchers interested in comparative genomics, PharmGKB contains an interface to VISTA (7) that allows genes in PharmGKB to be compared to the same genes in a mouse.”