VISTA: computational tools for comparative genomics

By Kelly A. Frazer, Lior S. Pachter, Alexander Poliakov, Edward M. Rubin, Inna Dubchak. Nucleic Acids Res., 2004

2,547 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/6a23ca4f444df5fee30d0b1bd12c5c73e62e93e9

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Citations in the corpus

MycoCosm portal: gearing up for 1000 fungal genomes (2013, methodology): “For example, predicted gene models are linked to annotation reports, while genome conservation tracks are linked to VISTA Point (23).”
The Arabidopsis Information Resource (TAIR): gene structure and function annotation (2007, methodology): “A track showing percent similarity between aligned Arabidopsis and Populus trichocarpa genomic sequences is provided through the VISTA plugin (2).”
VICTOR: genome-based phylogeny and classification of prokaryotic viruses (2017, methodology): “Some tools (Frazer et al. 2004; Ågren et al. 2012; Asare et al. 2015) were recently suggested by Krupovic et al.”
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons (2011, methodology): “Linear representations, like those that can be generated using Artemis Comparison Tool (ACT) [3], Genome2D [4], Combo [5], VISTA [6], Mauve [7], BugView [8] and Genomorama [9], have advantages in showing insertions and deletions between genomic sequences and certain programs, like Mauve and ACT, can”
Ensembl comparative genomics resources (2016, background): “These include the UCSC genome browser (14), which provides several sets of whole-genome pairwise and multiple alignments, as well as conservation data; and the VISTA Browser (15), which provides additional sets of multiple alignments (16) that can be viewed on either the VISTA browser itself or as a”
A Bioinformatician's Guide to Metagenomics (2008, methodology): “SNP-VISTA (124) is an adaptation of the comparative genomics tool VISTA (44), developed specifically to visualize SNPs in alignments.”
VISTA Enhancer Browser—a database of tissue-specific human enhancers (2006, background): “Complementary and partially overlapping sets of highly conserved elements are, for example, available through the VISTA Genome Browser (12), the UCSC Genome Browser (13), and the Dcode ECR browser (14).”
Rice SNP-seek database update: new SNPs, indels, and queries (2016, methodology): “Results of the pairwise genome alignments are view-able in the VISTA browser accessible through the SNP-Seek menu.”
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 (2006, positive): “edu/annotation/ciona/) using Vista software (Frazer et al., 2004).”
Phytozome: a comparative platform for green plant genomics (2011, methodology): “Each genome also undergoes whole genome alignment against a clade-informative subset of the other Phytozome genomes using the VISTA pipeline (32).”
Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing. (2017, methodology): “The regions 2,000bp upstream of the CLV3 CDS were scored for sequence homology to S. lycopersicum CLV3 using mVISTA (Frazer et al., 2004).”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, neutral): “shtml) (Frazer et al., 2004).”
Ensembl comparative genomics resources (2016, background): “These include the UCSC genome browser (14), which provides several sets of whole-genome pairwise and multiple alignments, as well as conservation data; and the VISTA Browser (15), which provides additional sets of multiple alignments (16) that can be viewed on either the VISTA browser itself or as a”