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Using the Generic Synteny Browser (GBrowse_syn)

McKay SJ, Vergara IA, Stajich JE. Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinformatics. Wiley Online Library; 2010;Chapter 9: Unit 9.12.
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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 9.9; Stein et at., 2002). The increasing number of sequenced genomes has 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 co-linear 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;; see Unit 1.8) and Arabidopsis (TAIR;; see Unit 1.11). 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, Mac OS X etc. GBrowse_syn is still under active development. This unit will cover installation and configuration as part of the current stable version of GBrowse (v1.71).