GBrowse_syn

http://gmod.org/wiki/GBrowse_syn

Methods

linear multiple view multiple scale multiple focus segregated no abstraction linear parallel arrangement between interconnection segment sparse type

Tool

Access Format web application
Supported Files fasta other
License GPL, Artistic License
Tool name

GBrowse_syn
Tool Link http://gmod.org/wiki/GBrowse_syn
Documentation http://gmod.org/wiki/GBrowse_syn

Paper

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.

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 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; www.wormbase.org; see Unit 1.8) and Arabidopsis (TAIR; www.arabidopsis.org; 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).