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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

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Versioning


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Documentation


Maintainer


  • person_outline Lincoln D. Stein

Publications for GBrowse

GBrowse citations

 (549)
library_books

The Sequenced Angiosperm Genomes and Genome Databases

2018
Front Plant Sci
PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] ) hosts assembled and annotated genomes from 59 angiosperm species, as well as other green lineage species, such as algae, moss, liverworts, selaginella (Goodstein et al., ). In addition to BLAST and Gbrowse tools, Phytozome also provide Biomart which allow users to annotate plant gene families, to study the evolution of plant gene families, to display genes in the genomic context (Goodstein et al […]

call_split

RNA Seq analysis validates the use of culture derived Trypanosoma brucei and provides new markers for mammalian and insect life cycle stages

2018
BMC Genomics
PMCID: 5879877
PMID: 29606092
DOI: 10.1186/s12864-018-4600-6
call_split See protocol

[…] 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 S […]

library_books

FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

2018
PMCID: 5872342
DOI: 10.3390/jof4010039

[…] . To send this run into a new history, check the box Send results to a new history (c). After the workflow has finished running, users can visualize the expression graphs (as BigWig files) in FungiDB GBrowse (). To import BigWig files into FungiDB GBrowse, click on the Display in FungiDB GBrowse link, which will become visible once a user clicks to expand the Bam to BigWig step in the workflow EuP […]

library_books

A functional SNP upstream of the ADRB2 gene is associated with COPD

2018
PMCID: 5859892
PMID: 29588580
DOI: 10.2147/COPD.S151153

[…] nd it is interesting to know whether this variant is correlated with the expression of ADRB2 in lymphoblastoid cells. To address this issue, we utilized eQTL browser (http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl/), which collected published eQTL data of lymphoblastoid cell lines (LCL) from four HapMap populations to search for potential association. Interestingly, a significant association betwee […]

library_books

Uneven recombination rate and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.)

2018
PLoS One
PMCID: 5844515
PMID: 29522524
DOI: 10.1371/journal.pone.0189597

[…] ualized in the Legume Information System (“LIS”; https://legumeinfo.org), in several contexts. The TOG-based map is viewable using CMap v. 1.01 [] with markers placed onto the Phaseolus vulgaris v1.0 GBrowse genome viewer, at https://legumeinfo.org/genomes/gbrowse/Pv1.0. Underlying data files are at the LIS database: https://legumeinfo.org/data/public/Phaseolus_vulgaris/mixed.map1.7PMp/. […]

library_books

Genome Wide Analysis Characterization and Evolution of SBP Genes in Fragaria vesca, Pyrus bretschneideri, Prunus persica and Prunus mume

2018
Front Genet
PMCID: 5841269
PMID: 29552026
DOI: 10.3389/fgene.2018.00064

[…] es in fifteen tissues was shown by heat map representation (Figure ). To explore the expression diversity of SBP family genes in F. vesca, we analyzed RNA-seq transcriptomic dataset obtained from SGR GBrowse database to investigate the expression pattern of each SBP gene during different development process (anther, Pollen, embryo, ghost, cortex, ovule, seedling, pollen, style, pith, wall, and lea […]

Citations

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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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