GBrowse syn

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GBrowse_syn running on WormBase.org
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GBrowse_syn is a synteny browser derived from GBrowse. It has many of the same zoom, pan and other genome navigation options as GBrowse. It designed as a synteny browser for three or more genomes. A working example can be seen at WormBase.

Documentation

Installation

  • GBrowse_syn uses much of the same infrastructure as GBrowse, in terms of species databases, configuration files, perl libraries, etc.
  • It comes as part of the GBrowse distribution, version 1.69 and later (GBrowse installation HOWTO...).
  • It differs in that databases and configuration for individual species are linked together via a central configuration file and a joining database that contains reciprocal alignments between all species represented in the browser.

Example alignment database

The files and scripts used to load the synteny browser at WormBase can be obtained from the WormBase ftp site.

Configuration

Configuration files

The main configuration file specifies the alignment database, the species to be included and their corresponding configuration files. This file ends with the extension ".synconf". Below is the configuration file used by WormBase.

The species configuration file contains information used by each species-specific database. This file has the extension ".syn". To avoid confusing GBrowse, select names for your GBrowse_syn configuration files that are not similar to the names or regular GBrowse configuration files. The configuration file used for C. briggsae on wormbase is shown below.



The Alignment database

Presentations

Facts about "GBrowse syn"RDF feed
Available on platformweb +
Date published2010 +
Has DOI10.1002/0471250953.bi0912s31 +
Has PMCIDPMC3162311 +
Has PMID20836076 +
Has URLhttps://github.com/GMOD/GBrowse +, http://mckay.cshl.edu/cgi-bin/gbrowse_syn/mercator/?search_src=Cbri%3Bname=chrX:620000..670000 +, http://www.arabidopsis.org/cgi-bin/gbrowse_syn/arabidopsis/?name=Chr1%3A8367000..8370501 +, http://dev.wormbase.org/db/seq/gbrowse_syn/compara?search_src=Cele%3Bname=X:1050001..1150000 + and http://solgenomics.net/gbrowse2/bin/gbrowse_syn/sol3/ +
Has authorMcKay SJ +, Vergara IA + and Stajich JE +
Has descriptionGBrowse_syn, or the Generic Synteny BrowseGBrowse_syn, or the Generic Synteny Browser, is a GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species. It can be used to view multiple sequence alignment data, synteny or co-linearity data from other sources against genome annotations provided by GBrowse. GBrowse_syn is included with the standard GBrowse package (version 1.69 and later). GBrowse package (version 1.69 and later). +
Has development statusactive +
Has download URLhttps://github.com/GMOD/GBrowse +
Has full nameGeneric Synteny Browser +
Has logoGBrowse_syn_logo.png +
Has publication detailsCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Chapter 9: Unit 9.12 +
Has software maturity statusbeta release +
Has support statusactive +
Has titleThe Arabidopsis Information Resource +, WormBase +, Sol Genomics + and Using the Generic Synteny Browser (GBrowse_syn). +
Has topicGBrowse syn +
Is open sourceYes +
Link typedownload +, source code +, demo server + and wild URL +
Published inCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] +
Release date1 January 2007 +
Tool functionality or classificationComparative genome visualization +
Written in languagePerl +
Has subobjectThis property is a special property in this wiki.GBrowse syn#https://github.com/GMOD/GBrowse +, GBrowse syn#http://mckay.cshl.edu/cgi-bin/gbrowse_syn/mercator/?search_src=Cbri;name=chrX:620000..670000 +, GBrowse syn#http://www.arabidopsis.org/cgi-bin/gbrowse_syn/arabidopsis/?name=Chr1%3A8367000..8370501 +, GBrowse syn#http://dev.wormbase.org/db/seq/gbrowse_syn/compara?search_src=Cele;name=X:1050001..1150000 + and GBrowse syn#http://solgenomics.net/gbrowse2/bin/gbrowse_syn/sol3/ +