GBrowse protocols

View GBrowse computational protocol

GBrowse statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Personal genomics Genome viewers chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

GBrowse specifications

Information


Unique identifier OMICS_00910
Name GBrowse
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input format BAM,SAM
Operating system Unix/Linux, Mac OS
Programming languages Perl
License Artistic License version 2.0, GNU General Public License version 3.0
Computer skills Advanced
Version 2.56
Stability Stable
Requirements
Apache
Source code URL https://metacpan.org/release/GBrowse
High performance computing Yes
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Lincoln D. Stein <>

Publications for GBrowse

GBrowse in pipelines

 (62)
2018
PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] genes, gene families, gene annotations, gene names, proteins, and mutant orderings. multiple web-integrated bioinformatics tools are also provided by tair. for examples, blast, wu-blast, fasta, gbrowse, synteny viewer, seqviewer, motif analysis, and chromosome map tool are powerful for visualization and comparative studies of genes and genome sequence at different scales. pathway maps […]

2018
PMCID: 5816337
PMID: 29483921
DOI: 10.3389/fpls.2018.00005

[…] , https://phytozome.jgi.doe.gov/pz/portal.html , http://cole-trapnell-lab.github.io/cufflinks/cufflinks/ , http://poplar.cgrb.oregonstate.edu/cgi-bin/gb2/gbrowse/poplar/ , http://combi.cs.colostate.edu/idiffir/ , http://www.bio-rad.com/webroot/web/pdf/lsr/literature/bulletin_6450.pdf , http://www.pacb.com/products-and-services/pacbio-systems , […]

2017
PMCID: 5909465
PMID: 29149280
DOI: 10.1093/dnares/dsx045

[…] gene annotation (itag 2.4, downloaded from the solgenomics website), and the cor and luc genomes. gene annotations of cor, luc, and heinz, were included in species-specific partition in the gbrowse database. a download data section allows sequences and data to be accessed upon request. association of all the genes among the three genomes from each annotation (heinz 1706, cor and luc) […]

2017
PMCID: 5292104
PMID: 27330039
DOI: 10.1016/j.margen.2016.06.004

[…] sequences was performed using clustalw2 (http://align.genome.jp) ()., synteny analyses were carried out using the generic genome browser (version 2.55) on salmobase (http://salmobase.org/cgi-bin/gb2/gbrowse/salmon_gbrowse_chr_ncbi/). the data source for the browser was ssal icsasg_v2. 100 kbp up- and downstream of each s. salar nfat5 paralogue were analysed along with the same region in esox […]

2017
PMCID: 5571531
PMID: 28244652
DOI: 10.1111/jcmm.13093

[…] with a minor allele frequency (maf) ≥0.05 within the han chinese population (chb) of beijing, china, as listed in the international hapmap project databank (http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/hapmap24_b36/; hapmap data rel 24/phasell nov08, on ncbi b36 assembly, dbsnp b126). then, linkage disequilibrium (ld) analysis with an r 2 threshold of 0.8 was performed with haploview 4.2 […]


To access a full list of citations, you will need to upgrade to our premium service.

GBrowse in publications

 (710)
PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] genes, gene families, gene annotations, gene names, proteins, and mutant orderings. multiple web-integrated bioinformatics tools are also provided by tair. for examples, blast, wu-blast, fasta, gbrowse, synteny viewer, seqviewer, motif analysis, and chromosome map tool are powerful for visualization and comparative studies of genes and genome sequence at different scales. pathway maps […]

PMCID: 5879877
PMID: 29606092
DOI: 10.1186/s12864-018-4600-6

[…] allow a maximum of 2 mismatches per 28 bp seed (galaxy version 1.1.2). sequencing depth and mapping coverage are provided in additional file . mapping to the genome was used to visualise the data on gbrowse; to estimate transcript abundance, reads were first mapped to coding sequences and unmapped reads were re-mapped to 3’ utrs. read counts for the annotated genes or 3’utr were extracted using […]

PMCID: 5940173
PMID: 29602811
DOI: 10.1534/g3.118.200205

[…] center (nih p40od018537) were used in this study. vienna drosophila resource center also provided valuable fly stocks. we used flybase release fb2017_06 () as a reference throughout and include gbrowse images in the supplemental data. we are also thankful for the support and input of all rolls lab members. we are especially grateful for the input from matthew shorey and dr. gregory kothe. […]

PMCID: 5947151
PMID: 29574807
DOI: 10.1111/nph.15089

[…] , where v g is the genotype variance, v e is the environmental variance and v t is the total variance of the trait of interest., gbrowser (http://mips.helmholtz-muenchen.de/gbrowse/plant/cgi-bin/gbrowse/brachy/) was used to investigate, in silico, the genomic region between the two markers flanking the qtl peak for possible candidate genes. the region on either side […]

PMCID: 5859077
PMID: 29555947
DOI: 10.1038/s41598-018-23124-9

[…] forms were represented by adding arabic numbers after “.” sign sequentially. the chromosomal location of all the putative gmdj-1 genes was identified from the soybase browser (http://soybase.org/gb2/gbrowse/gmax1.01/) to draw the chromosomal map. gene duplication was analyzed using plant genome duplication database (http://chibba.agtec.uga.edu/duplication/index/downloads) for soybean. divergence […]


To access a full list of publications, you will need to upgrade to our premium service.

GBrowse institution(s)
Ontario Institute for Cancer Research, Toronto, ON, Canada
GBrowse funding source(s)
Supported by grant #P41 G02223 from the National Human Genome Research Institute at the US National Institutes of Health, and by the Ministry of Economic Development and Innovation, Ontario (in part).

GBrowse reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GBrowse