Using the Generic Synteny Browser (GBrowse_syn)

Abstract

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 Unavailable; 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 Unavailable) and Arabidopsis (TAIR; http://www.arabidopsis.org; see UNIT Unavailable). 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). Curr. Protoc. Bioinform. 31:9.12.1‐9.12.25. © 2010 by John Wiley & Sons, Inc.