GBrowse

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The Generic Genome Browser (which is also occationally and incorrectly referred to as 'gbrowser') is a combination of database and interactive web page for manipulating and displaying annotations on genomes. The web browser has the following features.

  • Simultaneous bird's eye and detailed views of the genome.
  • Scroll, zoom, center.
  • Attach arbitrary URLs to any annotation.
  • Order and appearance of tracks are customizable by
    administrator and end-user.
  • Search by annotation ID, name, or comment.
  • Supports third party annotation using
    GFF formats.
  • Settings persist across sessions.
  • DNA and GFF dumps.

See gbrowse#demo a demo here

Tutorial

Scan through /nondrupal/tutorial/tutorial.html the tutorial that comes with the package to get a quick overview of its features.

Downloading and Installing

Download the source from the SourceForge download page., or see the installation instructions for information on installing from a binary distribution (most suitable on MS Windows platforms).

Getting the Latest & Greatest Version by CVS

There are many new features in the current development version which have not been released yet. To get the latest and greatest version, please use anonymous CVS. The recommended branch to use is "gbrowse-sessions" which is more stable than HEAD. Here is the recipe:


% cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login
CVS password: <hit return>
% cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co -r gbrowse-session Generic-Genome-Browser

Once you have successfully checked out the Generic-Genome-Browser distribution, you can simply perform a "cvs update" inside the directory to get recent changes.

You can also browse the GBrowse CVS here.

Demo

Select an organism and desired region; then press "Browse." This will take you to a live demo where you can browse the genomes of worm, yeast and fly. Mouse will be added when the assembly is published.

Browsable Genomes
C. elegans (worm) D. melanogaster (fly)

Chromosome I
Chromosome II
Chromosome III
Chromosome IV
Chromosome X



Arm 2L
Arm 2R
Arm 3L
Arm 3R
4
X
U



S. cerevisiae (yeast) H. sapiens (human)

Chromosome I
Chromosome II
Chromosome III
Chromosome IV
Chromosome V
Chromosome VI
Chromosome VII
Chromosome VIII
Chromosome IX
Chromosome XI
Chromosome XII
Chromosome XIII
Chromosome XIV
Chromosome XV
Chromosome XVI
Mitochondrium



Chromosome 1
Chromosome 2
Chromosome 3
Chromosome 4
Chromosome 5
Chromosome 6
Chromosome 7
Chromosome 8
Chromosome 9
Chromosome 10
Chromosome 11
Chromosome 12
Chromosome 13
Chromosome 14
Chromosome 15
Chromosome 16
Chromosome 17
Chromosome 18
Chromosome 19
Chromosome 20
Chromosome 21
Chromosome 22
Chromosome X
Chromosome Y



About the Database

GBrowse has a flexible adaptor system for running off various types of database. Standard adaptors include:

  • Flat file adaptors (in-memory, indexed) -- put your annotations in a directory and go!
  • Relational database adaptors -- Chado, Bio::DB::GFF, BioSQL
  • Network adaptors -- read annotations from GenBank, UCSC or Ensembl

Getting the Software

This is Open Source software, which is available for your own genome annotation projects. To get it, go to the SourceForge download page. Please report bugs to the SourceForge bug tracker. Please send questions to the GBrowse mailing list.


Facts about "GBrowse"RDF feed
Available on platformweb +
Date published2009 +, 2008 +, 2007 +, 2006 + and 2002 +
Has DOI10.1002/0471250953.bi0909s28 +, 10.1186/1471-2148-9-221 +, 10.1016/j.tube.2009.07.005 +, 10.1089/zeb.2008.0531 +, 10.1002/0471250953.bi0909s17 +, 10.1371/journal.pone.0000322 +, 10.1186/1751-0473-1-4 + and 10.1101/gr.403602 +
Has PMCIDPMC2755008 +, PMC1829191 +, PMC1636335 + and PMC187535 +
Has PMID19957275 +, 19732458 +, 19683474 +, 18554176 +, 18428797 +, 17389913 +, 17147784 + and 12368253 +
Has URLhttp://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ +, https://github.com/GMOD/GBrowse +, http://gbrowse.org +, http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ +, http://flybase.org/cgi-bin/gbrowse/dmel + and http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse +
Has authorDonlin MJ +, Cheng F +, Chen W +, Richards E +, Deng L +, Zeng C +, Bhardwaj A +, Bhartiya D +, Kumar N +, Open Source Drug Discovery Consortium +, Scaria V +, Meli R +, Prasad A +, Patowary A +, Lalwani MK +, Maini J +, Sharma M +, Singh AR +, Kumar G +, Jadhav V +, Sivasubbu S +, Schacherer J +, Ruderfer DM +, Gresham D +, Dolinski K +, Botstein D +, Kruglyak L +, Wilkinson M +, Stein LD +, Mungall C +, Shu S +, Caudy M +, Mangone M +, Day A +, Nickerson E +, Stajich JE +, Harris TW +, Arva A + and Lewis S +
Has descriptionGBrowse is a combination of database and iGBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Features include:
  • Simultaneous bird's eye and detailed views of the genome.
  • Scroll, zoom, center.
  • Use a variety of premade glyphs or create your own.
  • Attach arbitrary URLs to any annotation.
  • Order and appearance of tracks are customizable by administrator and end-user.
  • Search by annotation ID, name, or comment.
  • Supports third party annotation using GFF formats.
  • Settings persist across sessions.
  • DNA and GFF dumps.
  • Connectivity to different databases, including BioSQL and Chado.
  • Multi-language support.
  • Third-party feature loading.
  • Customizable plug-in architecture (e.g. run BLAST, dump & import many formats, find oligonucleotides, design primers, create restriction maps, edit features)
Note that the information on this page refers to GBrowse 2; GBrowse 1.x is recommended only for applications where legacy browser support is required and a single database is used.
is required and a single database is used. +
Has development statusactive +
Has full nameGeneric Genome Browser +
Has input formatGFF3 + and GFF2 +
Has licenceGPL2 + and Artistic License +
Has logoGBrowseLogo.png +
Has publication detailsCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Chapter 9: Unit 9.9 +, BMC evolutionary biology 9: 221 +, Tuberculosis (Edinburgh, Scotland) 89: 386-7 +, Zebrafish 5: 125-30 +, PloS one 2: e322 +, Source code for biology and medicine 1: 4 + and Genome research 12: 1599-610 +
Has software maturity statusmature +
Has support statusactive +
Has titleWormBase +, FlyBase +, HapMap +, Using the Generic Genome Browser (GBrowse). +, SNP@Evolution: a hierarchical database of positive selection on the human genome. +, TBrowse: an integrative genomics map of Mycobacterium tuberculosis. +, FishMap: a community resource for zebrafish genomics. +, Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. +, Gbrowse Moby: a Web-based browser for BioMoby Services. + and The generic genome browser: a building block for a model organism system database. +
Has topicGBrowse +
Is open sourceYes +
Link typedownload +, source code +, website + and wild URL +
Published inCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] +, BMC evolutionary biology +, Tuberculosis (Edinburgh, Scotland) +, Zebrafish +, PloS one +, Source code for biology and medicine + and Genome research +
Release date1 January 2001 +
Tool functionality or classificationGenome Visualization & Editing +
Written in languagePerl +
Has subobjectThis property is a special property in this wiki.GBrowse#http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ +, GBrowse#https://github.com/GMOD/GBrowse +, GBrowse#http://gbrowse.org +, GBrowse#http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ +, GBrowse#http://flybase.org/cgi-bin/gbrowse/dmel + and GBrowse#http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse +