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|SCRI Plant Bioinformatics Group

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GMOD Users

The following is a selection of the databases using GBrowse or Chado or some other popular component of GMOD. For a list of related publications see Publications. At the bottom of the page there is a list of GBrowse users.

Name Description Location Chado
A. fumigatus TIGR/Sanger Assembly http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/A_fumigatus_tigr_tel_100k
ANISEED Ascidian Network for In Situ Expression and Embryological Data http://crfb.univ-mrs.fr/ciona-bin/gbrowse/intestinalis/
AntonosporaDB http://gmod.mbl.edu/perl/site/antonospora01
ApiDB http://apidb.org/apidb/
ATIDB Arabidopsis http://atidb.org
Aureococcus http://gmod.mbl.edu/perl/site/aureococcus
AZM-to-BAC Viewer http://maizeapache.ddpsc.org/cgi-bin/gbrowse.cgi?source=01_azm2bac
AZM-to-Gene Viewer http://maizeapache.ddpsc.org/cgi-bin/gbrowse.cgi?source=02_azm2gene
BeeBase http://racerx00.tamu.edu/bee_resources.html
BeetleBase Gbrowse UI http://www.bioinformatics.ksu.edu/BeetleBase/ Yes
BGD Bovine Genome Database http://bovinegenome.org/
BioHealthBase BioDefense Public Health Database http://www.biohealthbase.org/GSearch/
Blochmannia pennsylvanicus http://gmod.mbl.edu/perl/site/blochmannia06
Bovine QTL Viewer http://bovineqtl.tamu.edu
Brachionus plicatilis A http://gmod.mbl.edu/perl/site/bplicatilisa
Brachionus plicatilis B http://gmod.mbl.edu/perl/site/bplicatilisb
Cattle EST Gene Family Database http://racerx00.tamu.edu/cgi-test/searchCattleDatabase.html
CGD Candida Genome Database http://www.candidagenome.org/cgi-bin/gbrowse/candida_20/
CGL Comparative Genomics Library http://www.yandell-lab.org/cgl/
ChromDB Plant Chromatin Database http://www.chromdb.org/
Chromosome 7 Annotation Project http://www.chr7.org/cgi-bin/gbrowse/gbrowse/chr7_v2
CryptoDB http://cryptodb.org
CSHLmpd Mammalian Promoter Database http://rulai.cshl.edu/cshlmpd/credit.html
Database of Genomic Variants http://projects.tcag.ca/variation/cgi-bin/gbrowse/hg17
DictyBase http://www.dictybase.org Yes
DroSpeGe http://insects.eugenes.org/DroSpeGe/
EcoCyc http://ecocyc.org/
Emiliania huxleyi http://gmod.mbl.edu/emiliania_huxleyi
Enterocytozoon bieneusi http://gmod.mbl.edu/perl/site/ebieneusi
Environmental Sampling Site 396, Fosmid 68 http://gmod.mbl.edu/perl/site/env396_fosmid68
Environmental Sampling Site 396, Fosmid 87 http://gmod.mbl.edu/perl/site/env396_fosmid87
Environmental Sampling Site 396, Fosmids_6_ 56 http://gmod.mbl.edu/perl/site/env396_fosmids_6_56
Environmental Sampling Site Loihi, Red Clone 1 http://gmod.mbl.edu/perl/site/envloihi_clone1
Environmental Sampling Site Loihi, Red Clone 2 http://gmod.mbl.edu/perl/site/envloihi_clone2
FlyBase http://www.flybase.org Yes
Fungal Comparitive Genomics http://fungal.genome.duke.edu/
Fungal Telomere Browser http://genome.kbrin.uky.edu/fungi_tel/browser.html
Gallus gallus Gallus gallus SAGE http://gmod.mbl.edu/perl/site/g_gallus
Gallus Genome Browser http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chicken
GeneDB Pathogen Sequenceing Unit http://www.genedb.org Yes
giardia14 http://gmod.mbl.edu/perl/site/giardia14
GiardiaDB http://gmod.mbl.edu/perl/site/giardia?page=intro
GrainGenes http://wheat.pw.usda.gov/
Gramene http://www.gramene.org
HapMap http://www.hapmap.org/cgi-perl/gbrowse/
Human 2q33 http://t1dbase.cimr.cam.ac.uk/cgi-bin/gbrowse/2q33/
Human Genome Segmental Duplication Database http://projects.tcag.ca/cgi-bin/duplication/dupbrowse/human_b36
IVDB Influenza Virus Database http://influenza.genomics.org.cn/
Leishmania tarentolae RNA editing database http://gmod.mbl.edu/gb/gbrowse/ltgrna
LIS Legume Information System http://www.comparative-legumes.org/
MAGI Maize Assembled Genomic Island http://magi.plantgenomics.iastate.edu/
Marinobacter aquaeolei http://gmod.mbl.edu/perl/site/marinobacter_jgi
Marinobacter aquaeolei FOSMID 38/33. http://gmod.mbl.edu/perl/site/marinobacter
MGI http://www.informatics.jax.org/
Non-Human Segmental Duplication Database http://projects.tcag.ca/xenodup/gbrowse.php
OMAP Oryza Map Alignment Project http://www.omap.org/
Oncorhynchus tshawytscha Chinook salmon SAGE http://gmod.mbl.edu/perl/site/salmontrout
OryGenesDB http://orygenesdb.cirad.fr/
Oryza Chromosome 8 http://map.lab.nig.ac.jp/cgi-bin/gbrowse/Oryza_chr8/
ParameciumDB http://paramecium.cgm.cnrs-gif.fr/ Yes
PeanutMap http://peanutgenetics.tamu.edu/cmap/
Philodina roseola http://gmod.mbl.edu/perl/site/proseola
PlantsDB MIPS PlantsDB http://mips.gsf.de/cgi-bin/proj/plant/gbrowse/synbrowse
PlasmoDB Plasmodium Genome Resource http://www.plasmodb.org/
PossumBase http://www.possumbase.org.nz/cgi-bin/gbrowse/mondom4/
PseudoCAP Pseudomonas Genome Database http://v2.pseudomonas.com/whats_new.jsp
PUMAdb Princeton Microarray Database, Chado http://puma.princeton.edu/
RGD Rat Genome Database http://rgd.mcw.edu
Schistosoma mansoni http://gmod.mbl.edu/perl/site/s_mansonigenome
Schistosoma mansoni EST http://gmod.mbl.edu/perl/site/s_mansoniest
SCRI Plant Bioinformatics Group http://bioinf.scri.sari.ac.uk/ Yes
SGD http://db.yeastgenome.org/cgi-bin/gbrowse/scgenome/
S. cerevisiae Proteome Browser http://db.yeastgenome.org/cgi-bin/gbrowse/scproteome/
SGD Lite http://sgdlite.princeton.edu/
SmedDB Planaria ESTs http://planaria.neuro.utah.edu/tools/tools.php Yes
SOL Genomics Network http://www.sgn.cornell.edu/ Yes
Soybase http://soybase.agron.iastate.edu/
Soybean Gbrowse Database http://soybeangenome.siu.edu/
Synechococcus 4320_2 http://gmod.mbl.edu/perl/site/syn_4320_2
Synechococcus CC9605 http://gmod.mbl.edu/perl/site/syn_cc9605
Synechococcus CC9902 http://gmod.mbl.edu/perl/site/syn_cc9902
Synechococcus RS9916 http://gmod.mbl.edu/perl/site/syn_rs9916
Synechococcus RS9917 http://gmod.mbl.edu/perl/site/syn_rs9917
Synechococcus WH5701 http://gmod.mbl.edu/perl/site/syn_wh5701
Synechococcus WH7805 http://gmod.mbl.edu/perl/site/syn_wh7805
T1DBase Type 1 Diabetes Database http://t1dbase.org/cgi-bin/dispatcher.cgi/Welcome/display
TAIR http://www.arabidopsis.org
TGD Tetrahymena Genome Database http://www.ciliate.org/help/Locus.shtml
TGI The Gene Index Project http://biocomp.dfci.harvard.edu/tgi/
TIGR The Institute for Genomic Research http://www.tigr.org Yes
TIGR Medicago BACs http://www.tigr.org/tigr-scripts/medicago/gbrowse_bacs.pl
TIGR Rice Genome Browser http://rice.tigr.org/tigr-scripts/osa1/gbrowse/ricegenomebrowser
ToxoDB Toxoplasma gondii database http://v3-0.toxodb.org/
TriAnnot BAC Viewer http://urgi.infobiogen.fr/projects/TriAnnot/GBrowse.php
Trypanosoma brucei brucei http://gmod.mbl.edu/perl/site/t_bruceibrucei02
Trypanosoma brucei brucei GenBank Entries http://gmod.mbl.edu/perl/site/t_bruceigenbank
Trypanosoma brucei brucei RNA editing database http://gmod.mbl.edu/gb/gbrowse/grna
Trypanosoma brucei gambiense http://gmod.mbl.edu/perl/site/t_bruceigambiense
Trypanosoma brucei rhodesiense http://gmod.mbl.edu/perl/site/t_bruceirhodesiense
Trypanosoma cruzi http://gmod.mbl.edu/perl/site/t_cruzi
UNH HCGS Tetraodon Genome Browser Gbrowse plus GFF http://hcgs.unh.edu/gbrowse/
VectorBase Chado, DAS, Apollo http://www.vectorbase.org Yes
Vicogenta Viewer for Comparing Genomes to Arabidopsis http://nypg.bio.nyu.edu/vicogenta/
wFleaBase Daphnia http://wfleabase.org/ Yes
WormBase http://www.wormbase.org
XanthusBase http://www.xanthusbase.org/ Yes
Xenbase http://www.xenbase.org/
Trichomona vaginalis http://www.uclaaccess.ucla.edu/UCLAACCESS/Web/Faculty.aspx?ri=58 Yes
Microarray data, Chado, H. sapiens http://genetics.ucla.edu/labs/nelson/ Yes
http://www.wicell.org Yes

GBrowse Users

This is a list of confirmed GBrowse users as of April 2004.

  • Agricultural Biotechnology Center, Hungary
  • BAWI, S. Korea
  • Baylor College of Medicine
  • Biocrates GmbH, Innsbruck
  • Brandeis University
  • Bristol-Meyers Squibb
  • British Columbia Centre for Diseaes Control
  • CIRAD, France
  • CSIRO, Australia
  • Cambridge University (multiple labs)
  • Center for Genomics & Bioinformatics, Stockholm
  • Center for Genomics and Bioinformatics, Stockholm
  • Centre de Genetique Moleculaire, CNRS
  • Cold Spring Harbor Laboratory (multiple labs)
  • Compugen
  • Concordia University, Canada
  • Cornell Medical School
  • Cornell University
  • DNA Landmarks, Inc.
  • Donald Danforth Plant Sciences Center
  • Duke University (multiple labs)
  • EMBL, Heidelberg
  • EuGenes (hacked copy)
  • Faculdade de Medicina de Ribeiro Preto, So Paulo
  • FlyBase
  • Foundation for Research and Technology, Crete
  • Fundao Hemocentro, Sao Paolo
  • Genoscope, France
  • GrainGenes
  • Harvard University
  • Hospital for Sick Kids, Toronto
  • Illinois Institute of Technology
  • Incyte Corporation
  • Inpharmatica, Ltd.
  • Institute for Systems Biology, Seattle
  • Institute of Molecular and Cell Biology, Singapore
  • International Rice Research Institute, Phillipines
  • John Innes Centre
  • KEGG
  • Kansas State University
  • Karolinska Institute
  • Kennedy Krieger Institute
  • Lawrence Berkeley Laboratories
  • Marine Biological Laboratories, Woods Hole
  • Massachusetts Institute of Technology (multiple labs)\
  • Mayo Institute
  • McGill University
  • Meat Animal Research Center, University of Nebraska
  • Medical University of South Carolina
  • Michigan State University
  • National Cancer Institute, Frederick Cancer Center
  • New York University (multiple labs)
  • North Carolina State University
  • Northern Illinois University
  • Northwestern University
  • Oklahoma State University
  • Open Informatics Consulting Corp.
  • Oxagen Corp.
  • Pasteur Institute, Paris
  • Pioneer Corporation
  • QIAGEN Operon Corp.
  • RIKEN (multiple labs)
  • RatDB
  • Regulome, Inc.
  • Rhobio (Bayer CropScience SA & Biogemma joint venture)
  • Rigshospitalet, Copenhagen
  • Rockefeller University
  • Roslin Institute, Edinburgh
  • Russian Academy Medical Sciences
  • Serono International Corp, Geneva
  • Simon Frasier University
  • South Africa National Bioinformatics Institute
  • Southern Illinois University
  • St. Jude Children's Research Hospital, Memphis
  • Stowers Institute for Medical Research
  • Texas A&M (multiple labs)
  • The Institute for Genome Research
  • Tulane University
  • Tulane University
  • University California Davis
  • University of Arizona (multiple labs)
  • University of British Columbia
  • University of California Santa Barbara
  • University of Georgia (multiple labs)
  • University of Minnesota
  • University of Muenster
  • University of New South Wales, Australia
  • University of Oklahoma (multiple labs)
  • University of Pennsylvania (multiple labs)
  • University of Southern California
  • University of Texas
  • University of Toronto
  • University of Virginia
  • University of Washington
  • Universitt Giessen
  • Universit de Lige, Belgium
  • Wageningen Universiteit & Researchcentrum, Netherlands
  • Washington University at St. Louis (multiple labs)
  • WormBase
  • deVGen, Belgium