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JBrowse specifications

Information


Unique identifier OMICS_00918
Name JBrowse
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Ian H Holmes <>

Additional information


https://github.com/GMOD/jbrowse/wiki

Information


Unique identifier OMICS_00918
Name JBrowse
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Javascript, Perl, Python, Shell (Bash)
License Artistic License version 2.0, GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.14.2
Stability Stable

Versioning


Add your version

Documentation


Maintainer


This tool is not maintained anymore.

Additional information


https://github.com/GMOD/jbrowse/wiki

Publications for JBrowse

JBrowse in pipelines

 (15)
2018
PMCID: 5759298
PMID: 29310588
DOI: 10.1186/s12864-017-4403-1

[…] 98,162 scaffolds and has been deposited at ddbj/ena/genbank under the accession peqf00000000. to obtain a more reasonable assembly for downstream bioinformatics analyses and for visualization in jbrowse [], scaffolds were filtered with the following parameters: scaffolds were removed when they contained fewer than 800 bases, or when 90% of the total scaffold length was contained […]

2018
PMCID: 5865747
PMID: 29570745
DOI: 10.1371/journal.pone.0194945

[…] carried out on the protein ncbi datasets of the m. truncatula, chickpea, and common bean genomes. the mlo annotations in the lentil draft genome assembly v1.2 can be accessed through the lentil jbrowse or blast function at http://knowpulse.usask.ca., the deduced amino acid sequences of the putative lcmlo genes were analyzed by several prediction programs to identify functional domains, […]

2017
PMCID: 5408436
PMID: 28465712
DOI: 10.1186/s13007-017-0181-7

[…] <1e−160, identity to query >70% and minimum sequence length of 200 residues). results were further curated manually by visual analysis of the blastp alignments and corresponding gene models in jbrowse (https://solgenomics.net/organism/nicotiana_benthamiana/genome) to eliminate potential partial protein due to mis-annotation. as a result, 36 additional candidates were retained for a total […]

2017
PMCID: 5463992
PMID: 28603666
DOI: 10.7717/peerj.3255

[…] to the upgma tree with the default color profile 1:4., identified genes from all mapk cascade families belonging to tomato, potato, pepper, and coffee were studied for exon-intron structure using jbrowse () and those belonging to eggplant by gsds 2.0 (). the number of exons in each one of them was recorded in the respective –. various characteristics of the genes were studied, including gene, […]

2017
PMCID: 5519730
PMID: 28729683
DOI: 10.1038/s41598-017-04768-5

[…] nucleotide reads were mapped to the annotated genome of strain ua159 (genbank accession: nc_004350.2). samtools software was used to divide the reads in each according strand. for visualization, jbrowse viewer was employed. differential expression analyses of samples with and without xip were determined based on the mapped read profiles using a perl script. the read counts were subjected […]


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JBrowse in publications

 (136)
PMCID: 5921565
PMID: 29699480
DOI: 10.1186/s12859-018-2160-z

[…] visualization strategies, as is the case for epigenomics data such as dna base modifications, small non-coding rnas, and histone modifications., we present a set of plugins for the genome browser jbrowse that are targeted for epigenomics visualizations. specifically, we have focused on visualizing dna base modifications, small non-coding rnas, stranded read coverage, and sequence motif […]

PMCID: 5902831
PMID: 29661130
DOI: 10.1186/s12711-018-0390-1

[…] whether the gene is known to cause early lethality in mice obtained from the mgi database release 6.10 (i.e. phenotypes from null-mutant mice) []. we manually examined all predicted el variants in jbrowse [] to exclude false positives that derived from sequencing and mapping errors. significant differences in hatchability between carrier by carrier versus carrier by non-carrier phenotypes […]

PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] genome database (peargenome.njau.edu.cn) only provide data download. the ash tree (hymenoscyphus fraxinea and agrilus planipennis) genome database (ashgenome.org/) includes the blast, jbrowse tools, and data download service. the jujube (ziziphus jujuba) genome database (jujube.genomics.cn/page/species/index.jsp) has tools such as gene search, mapview and blast. the limited […]

PMCID: 5889549
PMID: 29625550
DOI: 10.1186/s12864-018-4606-0

[…] were mapped according to shearer et al. []. to map tomato sequences onto chromosomes, gene position information was acquired from phytozyme (https://phytozome.jgi.doe.gov/pz/portal.html) and jbrowse at sgn. mapping of g-lecrks onto tomato chromosomes was performed manually using ncbi map viewer (https://www.ncbi.nlm.nih.gov/genome/gdv/). tomato predicted kinase domain sequences […]

PMCID: 5870498
PMID: 29587634
DOI: 10.1186/s12864-018-4538-8

[…] ncbi sequence read archive. accession numbers are as follows: [ncbi sequence read archive: srx156386, srx157659, srx157660, srx157661, srx157683 and srx158075]. the sequence data is viewable using jbrowse on www.pseudomonas.com., the online version of this article (10.1186/s12864-018-4538-8) contains supplementary material, which is available to authorized users., pseudomonas aeruginosa […]


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JBrowse institution(s)
Department of Bioengineering, University of California at Berkeley, Berkeley, CA, USA
JBrowse funding source(s)
Supported by the National Institutes of Health/National Human Genome Research Institute (R01-HG004483).

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