The generic genome browser: a building block for a model organism system database.

By Lincoln D. Stein, C. Mungall, S. Shu, M. Caudy, Marco Mangone, Allen Day, E. Nickerson, Jason E. Stajich, T. Harris, Adrian Arva and 1 more. Genome Research, 2002

1,205 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/267307f9ec89ce6f69e7fa9e8f24d9e9a0febef0

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

The Comprehensive Antibiotic Resistance Database (2013, methodology): “1) (14) configured to use the Bio:DB: Das:Chado adaptor to have GBrowse read data directly from Chado.”
Tabix: fast retrieval of sequence features from generic TAB-delimited files (2011, positive): “It is particularly useful for manually examining local genomic features on the command line and enables genome viewers to support huge data files and remote custom tracks over networks.”
Modelling the impacts of pests and diseases on agricultural systems (2017, background): “For example, in genomics, synteny analyses produces analytical results far beyond that which could be expected from the informal aggregation of fragmented results (Tatusov et al., 2000; Stein et al., 2002).”
bioDBnet: the biological database network (2009, background): “Wherever applicable the reports have links to polyBrowse (http://pbrowse2. abcc.ncifcrf.gov), a gbrowse-based browser (Stein et al., 2002), the UCSC genome browser (http://genome.ucsc.edu, Kent et al., 2002) forvisualizingdataonthechromosomesandtoDAVID(http://david. abcc.ncifcrf.gov, Huangda et…”
A survey of sequence alignment algorithms for next-generation sequencing (2010, methodology): “They all output alignments in the SAM format [62], the emerging standard alignment format which is widely supported by alignment viewers such as GBrowse [63], LookSeq [64], Tablet [65], BamView [66], Gambit (http://tinyurl.”
SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny (2008, methodology): “The SUPERFAMILY DAS server provides protein domain assignment details in XML format for use by DAS clients such as gbrowse [the GMOD genome browser (29)] and DASTY (http://www.ebi.ac.uk/dasty/).”
JBrowse: a dynamic web platform for genome visualization and analysis (2016, background): “…JavaScript genome browsers such as Biodalliance [4], pileup.js [5], and Galaxy ’ s Trackster [6]; other (Common Gateway Interface (CGI)-based) web-facing browsers such as the UCSC Genome Browser [7], Ensembl ’ s browser [8], and GBrowse [9]; and desktop browsers such as IGV [10] and IGB [11].”
FungiDB: an integrated functional genomics database for fungi (2011, methodology): “in the right-hand column of Figure 1C, including access to the GMOD genome browser (30), BLAST (31), the sequence retrieval tool, access to web services searches and a list of fungal-related literature (based on PubMed searches).”
Saccharomyces Genome Database: the genomics resource of budding yeast (2011, methodology): “SGD uses the GBrowse genome browser (24) to display diverse types of genomic information, with our most recent efforts focusing on chromatin structure, including histone modifications, histone variants and nucleosome organization; chromosomal maintenance sites for meiotic recombination and origins o”
The Arabidopsis Information Resource: Making and Mining the ‘Gold Standard’ Annotated Reference Plant Genome (2015, methodology): “GBrowse, a component of the GMOD project (Stein et al ., 2002) provides views of additional data types not available in SeqViewer including methylation and phosphorylation patterns, repeat regions, and orthologous genes in other species, as well as additional expression data types including…”
The Sugarcane Genome Challenge: Strategies for Sequencing a Highly Complex Genome (2011, methodology): “Genes and TE automatic annotations are stored into the GNPannot chado database (PostgreSQL) (Mungall and Emmert 2007) and can be easily visualized with a gbrowse web graphic interface ( Stein et al. 2002 ).”
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data (2013, methodology): “An install of the Generic Genome Browser (Stein et al. 2002) providing 83 tracks of annotation including the MSU Rice Genome Annotation Project Release 7 data is available at http://rice. plantbiology.msu.edu/cgi-bin/gbrowse/rice/.”
The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. (2005, background): “Although other browsers for comparative genomics have been developed (see Stein et al. 2002; Sherman et al. 2004), they have three limitations that make them inappropriate for our purposes.”
Development of Genetic and Genomic Research Resources for Brachypodium distachyon, a New Model System for Grass Crop Research (2008, neutral): “BrachyBase is based on the GMOD genome browser (gbrowse; Stein et al., 2002), and the current prototype version uses the TIGR japonica rice genome assemblies (International Rice Genome Sequencing Project, 2005) as a surrogate genome scaff old for Brachypodium sequence alignments (Fig.”
Apollo: a sequence annotation editor (2002, methodology): “In practice, both the Berkeley and Ensembl groups use Perl for internet-based data access [39] and Java for locally resident applications.”
FlyBase: genes and gene models (2004, background): “GBrowse (18) is a configurable genome viewer that allows the presentation of both molecularly mapped and cytologically mapped data (http://www.”