VISTA Browser protocols

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VISTA Browser specifications

Information


Unique identifier OMICS_00948
Name VISTA Browser
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline VISTA Browser Group <>

Publication for VISTA Browser

VISTA Browser in pipelines

 (3)
2015
PMCID: 4551851
PMID: 26313368
DOI: 10.1371/journal.pone.0136666

[…] sep 2011), medaka (hdrr, oct 2005) and spotted gar (lepocu1, insdc assembly, dec 2011). global pairwise alignment was carried out using shuffle-lagan [], and the results were visualized using the vista browser []. conserved transcription factor binding consensus sequences were identified using rvista [] and visual inspection of the aligned sequences., in previous studies, we identified eight […]

2015
PMCID: 4624090
PMID: 26543346
DOI: 10.4137/EBO.S15364

[…] as blat (blast-like alignment tool) in order to identify homology. the data were then processed and globally aligned using the mlagan (multiple alignment) program. alignments were visualized in the vista browser by defining the colors and patterns of peaks and valleys. next, the conservation of the region was evaluated. for the conservation evaluation, we used the program’s default parameters […]

2007
PMCID: 2174922
PMID: 17986329
DOI: 10.1186/1471-2229-7-59

[…] microarray analyses. sequence conservation and microsynteny analysis of populus gene models with populus homeologous (duplicated) genomic regions and the arabidopsis genome was conducted using the vista browser tool with default curve calculation parameters; nucleotide sequence 'conservation identity' of 70% and 'minimum conservation width' of 100 bp []. one gene model per locus, […]


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VISTA Browser in publications

 (47)
PMCID: 5773237
PMID: 29346379
DOI: 10.1371/journal.pone.0189810

[…] a band of 889 bp., to visualize regions of conservation surrounding the lafa gene in other burkholderia species, precomputed alignments were analyzed for conservation surround ak34_rs07895 in the vista browser located at integrated microbial genomes website: (https://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=vista&page=vista). default parameters for conservation were used. microbial […]

PMCID: 5746500
PMID: 29302202
DOI: 10.5607/en.2017.26.6.350

[…] promoter region of the haldh1l1 gene and compare with other species, we extracted and aligned the chromosomal locus of aldh1l1 for human, mouse, rat, cow, marmoset and rhesus monkey using the vista-browser2 (). we then selected the putative haldh1l1 promoter region of 1.3 kb including the upstream sequences from position −1028 to the transcription start site. the size is chosen to fit […]

PMCID: 5670250
PMID: 29101371
DOI: 10.1038/s41598-017-15153-7

[…] doris wedlich)., for phylogenetic footprinting x. tropicalis was used as a reference genome and was compared with human, mouse, rat and chick genomes using ecr browser (http://ecrbrowser.dcode.org), vista browser (http://genome.lbl.gov/vista/index.shtml) and pipmaker (http://pipmaker.bx.psu.edu/pipmaker/)., all relevant data analyzed during this study are included in this published article., , […]

PMCID: 5546707
PMID: 28742084
DOI: 10.1371/journal.pgen.1006933

[…] the analogous human regions of previously identified functional murine cns regions [] by taking the top 20 most conserved intergenic sites between mouse and human in the lcr region using the vista browser (http://pipeline.lbl.gov/cgi-bin/gateway2). genoskyline-plus scores in the 20 cns sites and their 200-bp flanking regions were compared across different cell types., summary statistics […]

PMCID: 5507538
PMID: 28704421
DOI: 10.1371/journal.pone.0180579

[…] are sites including 5’-tagtacaccccgatt-3’ at site -1995, 5’-gagaaaacaatgctt-3’at position -1977 and 3’-aaggacttatagaaa-5’ at site -1933 (). accordingly, comparative genomic analysis using the vista browser (http://genome.lbl.gov/vista/index.shtml), showed high conservation among the species for arso-sox2ot sequence ( and ). data from suggested that arso-sox2ot sequence containing the ar […]


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VISTA Browser institution(s)
Lawrence Berkeley National Laboratory, USA

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