The Generic Genome Browser: A Building Block for a Model Organism System Database

Abstract

The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.Model organism system databases (MODs) are a vital tool for scientific research. They share a common set of tasks: to collect and curate data from the scientific literature such as mutations, alleles, genetic and physical maps, and phenotypes; to integrate this information with the results of large-scale experiments such as microarray studies, SNP screens, and protein-interaction studies; to provide reagent resources such as stocks, genetic constructs, and clones; and, lastly, to provide a common nomenclature for gene symbols, anatomic terms, and other elements of the scientific vocabulary. By integrating, and in some cases reanalyzing, these data, MODs are able to greatly enhance their value. This information is made available to the research community via a Web site that also serves as a nexus for discussions, announcements of interest to the community, and data submissions.

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

“…Additionally, we specifically designed a browser database using GBrowse (Stein et al, 2002;version 1.70) to visualize all data in this study (Supplemental Fig. S1).…”

COLdb, a database linking genetic data to molecular function in fibrillar collagens

“…GBROWSE functionality is described elsewhere [Stein et al, 2002] and documented in online help pages provided on the COLdb Web site. Here, we briefly highlight some of the key functions of the software and the collagen-specific features.…”

“…The data can be viewed as annotations on the collagen protein sequences using an interactive, Web-based graphical user interface developed with the GBROWSE package [Stein et al, 2002]. GBROWSE functionality is described elsewhere [Stein et al, 2002] and documented in online help pages provided on the COLdb Web site.…”

In Vitro Generation of Human High-Density-Lipoprotein-Resistant Trypanosoma brucei brucei

“…The 21-bp SAGE tags were mapped to assembly contigs based on exact sequence matches. Tags were then visualized in a generic model organism database using the Gbrowse interface (61) in the context of genome sequences and predicted open reading frames. As SAGE tags are generated from the most 3Ј NlaIII restriction site of transcripts, tags with significant differential expression among the SAGE libraries were manually assigned to predicted genes based on their position relative to predicted ORFs.…”