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Citations per year

Number of citations per year for the bioinformatics software tool VISTA Browser
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Tool usage distribution map

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Protocols

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 No

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Publication for VISTA Browser

VISTA Browser citations

 (56)
library_books

A putative lateral flagella of the cystic fibrosis pathogen Burkholderia dolosa regulates swimming motility and host cytokine production

2018
PLoS One
PMCID: 5773237
PMID: 29346379
DOI: 10.1371/journal.pone.0189810

[…] oduce 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 genomes c […]

library_books

AAV Mediated Astrocyte Specific Gene Expression under Human ALDH1L1 Promoter in Mouse Thalamus

2017
PMCID: 5746500
PMID: 29302202
DOI: 10.5607/en.2017.26.6.350

[…] opriate 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 into […]

call_split

Identification of novel cis regulatory elements of Eya1 in Xenopus laevis using BAC recombineering

2017
Sci Rep
PMCID: 5670250
PMID: 29101371
DOI: 10.1038/s41598-017-15153-7
call_split See protocol

[…] 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/). […]

library_books

Systematic tissue specific functional annotation of the human genome highlights immune related DNA elements for late onset Alzheimer’s disease

2017
PLoS Genet
PMCID: 5546707
PMID: 28742084
DOI: 10.1371/journal.pgen.1006933

[…] entified 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. […]

library_books

Transcriptional role of androgen receptor in the expression of long non coding RNA Sox2OT in neurogenesis

2017
PLoS One
PMCID: 5507538
PMID: 28704421
DOI: 10.1371/journal.pone.0180579

[…] utative 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 D […]

library_books

Systematic identification of gene family regulators in mouse and human embryonic stem cells

2016
Nucleic Acids Res
PMCID: 4872113
PMID: 27084933
DOI: 10.1093/nar/gkw259

[…] TA4 with the VISTA database, but not its presence in the enhancer associated cluster, and may stem from a the fact that our analysis was restricted only to ESCs while the enhancers extracted from the VISTA browser were not. Similarly, the clustering of HDAC2 within the enhancer cluster, while not showing a high correlation to the VISTA enhancers set, might originate from the association of the NuR […]


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

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