Introduction

Genome Browsers are software that allow the user to view genome annotations in the context of a reference sequence, such as a chromosome, contig, scaffold, etc. The Generic Genome Browser (GBrowse) is an open-source genome browser package developed as part of the Generic Model Database Project (see UNIT ; Stein et al., 2002). The increasing number of sequenced genomes has led to a corresponding growth in the field of comparative genomics, which requires methods to view and compare multiple genomes. Using the same software framework as GBrowse, the Generic Synteny Browser (GBrowse_syn) allows the comparison of colinear regions of multiple genomes using the familiar GBrowse-style Web page. Like GBrowse, GBrowse_syn can be configured to display any organism, and is currently the synteny browser used for model organisms such as C. elegans (WormBase; http://www.wormbase.org; see UNIT 1.8) and Arabidopsis (TAIR; http://www.arabidopsis.org; see UNIT 1.1). GBrowse_syn is part of the GBrowse software package and can be downloaded from the Web and run on any Unix-like operating system, such as Linux, Solaris, or MacOS X. GBrowse_syn is still under active development. This unit will cover installation and configuration as part of the current stable version of GBrowse (v. 1.71).

Publications

  1. Using the Generic Synteny Browser (GBrowse_syn).
    Cite this
    McKay SJ, Vergara IA, Stajich JE, 2010-09-01 - Current protocols in bioinformatics

Credits

  1. Sheldon J McKay
    Developer

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States of America

  2. Ismael A Vergara
    Developer

  3. Jason E Stajich
    Investigator

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Summary
AccessionBT000273
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByJason E Stajich