Using the Generic Synteny Browser (GBrowse_syn)

McKay, S. J., Vergara, I. A., Stajich, J. E. (2010) Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinformatics, Chapte. Unit 9 12. ISSN 1934-340X (Electronic) 1934-3396 (Linking)

[img]
Preview
PDF (Using the Generic Synteny Browser (GBrowse_syn))
Using_the_Generic_Synteny_Browser_(GBrowse_syn).pdf

Download (2820Kb)
URL: http://www.ncbi.nlm.nih.gov/pubmed/20836076

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 ; 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).

Item Type: Paper
Additional Information: 10.1002/0471250953.bi0912s31
Subjects: bioinformatics > genomics and proteomics > databases > database construction
bioinformatics > genomics and proteomics > databases > database optimization
bioinformatics > genomics and proteomics > annotation > gene expression profiling annotation
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > annotation > map annotation
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > computers > computer software
CSHL Authors:
Depositing User: CSHL Librarian
Date Deposited: 03 Oct 2011 16:13
Last Modified: 29 Nov 2011 20:01
PMCID: PMC3162311
URI: http://repository.cshl.edu/id/eprint/15478

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving