JContextExplorer protocols

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JContextExplorer specifications


Unique identifier OMICS_14451
Name JContextExplorer
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data Annotated genome
Input format TXT
Output data Representations of context tress
Output format JPG, PNG, EPS
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 3.0
Stability Stable
BioJava, EpsGraphics
Maintained Yes



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  • person_outline Marc Facciotti <>

Publication for JContextExplorer

JContextExplorer in pipeline

PMCID: 4230888
PMID: 25393412
DOI: 10.1371/journal.pgen.1004784

[…] analysis, building of molecular marker sets and phylogenetically informed re-annotation. these annotations can be accessed as a loadable “popular genome set” through the genome context viewer jcontextexplorer as well as a custom mysql database (see for instructions). the rast annotation system was particularly useful in enabling comparison of our genomes with previously sequenced […]

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JContextExplorer in publications

PMCID: 4927057
PMID: 27355474
DOI: 10.1371/journal.pgen.1006145

[…] examine the genomic context of e. coli cdi gene clusters, we used the cdia sequence from e. coli ec93 to query the escherichia taxon using blast. the top 961 hit sequences were then analyzed using jcontextexplorer to compare cdi gene neighborhoods []. this analysis revealed that a large number of e. coli cdi loci are harbored within genomic islands inserted at the 3´-ends of various trna genes […]

PMCID: 4915679
PMID: 27327432
DOI: 10.1371/journal.pone.0156543

[…] had a full complement of crte, crtb, and crti, presence or absence of crty and brp was used to represent retinal biosynthesis ability., genomic context of haloarchaeal orps was investigated using jcontextexplorer []. haloarchaeal genomes can be loaded using the “retrieve popular genome set” function. annotations associated with this genome set were done using the rast annotation service [] […]

PMCID: 4230888
PMID: 25393412
DOI: 10.1371/journal.pgen.1004784

[…] of homologous proteins representing distinct protein families. we have made genome data and homology clusters for all 80 sequenced haloarchaea available through the genome context visualization tool jcontextexplorer (see for access instructions). we believe that this genomic data will provide a rich source of information for the archaeal, genomics, evolutionary biology, and systems biology […]

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JContextExplorer institution(s)
Department of Biomedical Engineering, University of California, Davis, CA, USA; Genome Center, University of California, Davis, CA, USA; Microbiology Graduate Group, University of California, Davis, CA, USA
JContextExplorer funding source(s)
This work was supported by the NSF FE-094953 and startup funds to MTF

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