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 http://search.cpan.org/dist/GBrowse/
High performance computing Yes
Maintained Yes

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Maintainer


  • person_outline Lincoln D. Stein <>

GBrowse articles

GBrowse citations

 (18)
2017
PMCID: 5292104

[…] (http://align.genome.jp) (larkin et al., 2007)., 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 lucius (ncbi […]

2016
PMCID: 5080602

[…] the orthologs of the genes present in the extended breakpoint regions of the d. subobscura inversions in drosophila species other than d. melanogaster. orthologs were initially identified using gbrowse searches. however, the lack of annotation or misannotation of some genes in one or more of the eleven species, as well as a different relative orientation of the genes included […]

2016
PMCID: 4916121

[…] be browsed online from the official website of the ganit labs, bio-it centre, institute of bioinformatics and applied biotechnology, (http://115.119.161.46:96/cgi-bin/gb2/gbrowse/neemv2/) using gbrowse 2.0. after the neem genome was prepared, clean reads from the a. indica libraries (y1–3) were aligned to the reference genome using tophat2 (kim et al. 2013). briefly, the mapping process […]

2016
PMCID: 5041464

[…] (http://www.yeastgenome.org) as backbones. native transcription factor binding sites were identified using chip-derived data (15), either from visualizing them using the yeast genome database's gbrowse tool with the relevant track, or by searching the promoter sequences in the yetfasco database (16) for the motifs listed in table 1. when choosing binding sites to screen for or modify, […]

2016
PMCID: 5043505

[…] result in reduction in the cost of lignocellulosic biofuel production., protein sequences of 53 populus trichocarpa laccases were collected from phytozome v10.3 [http://www.phytozome.net/cgi-bin/gbrowse/poplar/]: populus trichocarpa v3.0. protein sequences of laccases from arabidopsis thaliana were collected from tair [http://www.arabidopsis.org]. all other laccase sequences from other plant […]

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).

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