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

  title={The generic genome browser: a building block for a model organism system database.},
  author={Lincoln Stein and Chris J. Mungall and Shengqiang Shu and Michael Caudy and Marco Mangone and Allen Day and Elizabeth Nickerson and Jason E. Stajich and Todd W. Harris and Adrian Arva and Suzanna E. Lewis},
  journal={Genome research},
  volume={12 10},
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… 

Figures from this paper

Using the Generic Genome Browser (GBrowse)

  • M. Donlin
  • Biology, Computer Science
    Current protocols in bioinformatics
  • 2009
The Generic Genome Browser (GBrowse) is an open‐source browser developed as part of the Generic Model Organism Database project (Stein et al., 2002).

Using the Generic Synteny Browser (GBrowse_syn)

The Generic Synteny Browser (GBrowse_syn) allows the comparison of colinear regions of multiple genomes using the familiar GBrowse‐style Web page and can be configured to display any organism.

Choosing a genome browser for a Model Organism Database: surveying the Maize community

The survey’s outcomes are documented, functionalities of available genome browser software platforms are reviewed, and the rationale for choosing the GBrowse software suite for MaizeGDB is offered.

TGAC Browser: An open-source genome browser for non-model organisms

Genome browsers play a vital role to provide visualisation for genomic data. It is often the case that bespoke genome browser customisations are required between different research groups, with an

Setting Up the JBrowse Genome Browser

This unit describes how to obtain the JBrowse software, set it up on a Linux or Mac OS X computer running as a Web server, and incorporate genome annotation data from multiple sources into J Browse.

Java-based application framework for visualization of gene regulatory region annotations

MOTIVATION The genome sequences of several organisms are either complete, or being sequenced. Each genome needs to be integrated with various types of annotations, e.g. locations of genes, promoters

The UCSC genome browser and associated tools

The UCSC Genome Browser is a graphical viewer for genomic data that presents visualization of annotations mapped to genomic coordinates, and the ability to juxtapose annotations of many types facilitates inquiry-driven data mining.

ABrowse - a customizable next-generation genome browser framework

A general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support, and rich user functions and flexible customization approaches is developed.

Genomes as geography: using GIS technology to build interactive genome feature maps

An interactive genome sequence feature map for the mouse genome is implemented in GenoSIS, an application that uses ArcGIS, a commercially available GIS software system that supports the generation of custom genome maps in response to complex queries about genome features based on both their attributes and locations.

CompaGB: An open framework for genome browsers comparison

A community-based framework based on the implementation of industry promoted software qualification method (QSOS) adapted for genome browser evaluations, and a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations is proposed.



The human genome browser at UCSC.

A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at

The Ensembl genome database project

The Ensembl ( database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic

Genotator: a workbench for sequence annotation.

Genotator is a workbench for automated sequence annotation and annotation browsing that provides an intuitive way to identify the significant regions (for example, probable exons) in a sequence.

The Distributed Annotation System

The Distributed Annotation System (DAS) allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software.

The FlyBase database of the Drosophila genome projects and community literature.

  • Biology
    Nucleic acids research
  • 2003
A complete revision of the annotations of the now-finished euchromatic genomic sequence has been completed and there are many points of entry to the genome within FlyBase, most notably through maps, gene products and ontologies, structured phenotypic and gene expression data, and anatomy.

Genome annotation assessment in Drosophila melanogaster.

This experiment presents the first assessment of promoter prediction techniques for a significant number of genes in a large contiguous region and discovered that the promoter predictors' high false-positive rates make their predictions difficult to use.

The Bioperl toolkit: Perl modules for the life sciences.

The overall architecture of the Bioperl toolkit is described, the problem domains that it addresses, and specific examples of how the toolkit can be used to solve common life-sciences problems are given.

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000

The Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT, is described.

Flexible sequence similarity searching with the FASTA3 program package.

The FASTA3 and FASTA2 packages provide a flexible set of sequence-comparison programs that are particularly valuable because of their accurate statistical estimates and high-quality alignments.

GenBank. Nucleic Acids Res

  • GenBank. Nucleic Acids Res
  • 2002