Difference between revisions of "GBrowse syn"

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==Configuration==
 
==Configuration==
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===Configuration files===
 
The main configuration file specifies the alignment database, the species to be included and their corresponding configuration files.  An example from wormbase is shown below.
 
The main configuration file specifies the alignment database, the species to be included and their corresponding configuration files.  An example from wormbase is shown below.
 
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===Configuration files===
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===The Alignments database===
 
===The Alignments database===
 
==Examples==
 
==Examples==

Revision as of 21:07, 21 December 2007

GBrowse_syn running on WormBase.org
View at full resolution

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

Documentation

GBrowse_syn uses the same infrastructure as Gbrowse, in terms of species databases, etc. It differs in that databases and configuration for indivaidual species are linked together via a central configuration file and an alignment database.

Configuration

Configuration files

The main configuration file specifies the alignment database, the species to be included and their corresponding configuration files. An example from wormbase is shown below.


The Alignments database

Examples

Retrieved from "http://gmod.org/mediawiki/index.php?title=GBrowse_syn&oldid=3714"
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 Browse … GBrowse_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/ +