GMOD Users
From GMOD
Revision as of 23:10, 28 February 2013 by Girlwithglasses (Talk | contribs)
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 | URL | Chado | Year added/checked |
---|---|---|---|---|
TreeTFDB | transcription factors (TF) of papaya (Carica papaya), jatoropha (Jatropha curcas), cassava (Manihot esculenta), poplar (Populus trichocarpa), castor bean (Ricinus communis) and grape vine (Vitis vinifera) | http://treetfdb.bmep.riken.jp/index.pl | 2013 | |
Eimeria transcript database | Annotated transcripts of protozoan parasites of the genus Eimeria | http://www.coccidia.icb.usp.br/eimeriatdb/ | 2013 | |
A. fumigatus TIGR/Sanger Assembly | http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/A_fumigatus_tigr_tel_100k | 200x | ||
ANISEED | Ascidian Network for In Situ Expression and Embryological Data | http://crfb.univ-mrs.fr/ciona-bin/gbrowse/intestinalis/ | 200x | |
AntonosporaDB | http://gmod.mbl.edu/perl/site/antonospora01 | 200x | ||
AphidBase | Pea aphid genome | http://www.aphidbase.com/ | Yes | 200x |
ApiDB | http://apidb.org/apidb/ | 200x | ||
ATIDB | Arabidopsis | http://atidb.org | 200x | |
Aureococcus | http://gmod.mbl.edu/perl/site/aureococcus | 200x | ||
AZM-to-BAC Viewer | http://maizeapache.ddpsc.org/cgi-bin/gbrowse.cgi?source=01_azm2bac | 200x | ||
AZM-to-Gene Viewer | http://maizeapache.ddpsc.org/cgi-bin/gbrowse.cgi?source=02_azm2gene | 200x | ||
BeeBase | http://racerx00.tamu.edu/bee_resources.html | 200x | ||
BeetleBase | Gbrowse UI | http://www.bioinformatics.ksu.edu/BeetleBase/ | Yes | 200x |
BGD | Bovine Genome Database | http://bovinegenome.org/ | 200x | |
BioHealthBase | BioDefense Public Health Database | http://www.biohealthbase.org/GSearch/ | 200x | |
Blochmannia pennsylvanicus | http://gmod.mbl.edu/perl/site/blochmannia06 | 200x | ||
Bovine QTL Viewer | http://bovineqtl.tamu.edu | 200x | ||
Brachionus plicatilis A | http://gmod.mbl.edu/perl/site/bplicatilisa | 200x | ||
Brachionus plicatilis B | http://gmod.mbl.edu/perl/site/bplicatilisb | 200x | ||
Cattle EST Gene Family Database | http://racerx00.tamu.edu/cgi-test/searchCattleDatabase.html | 200x | ||
CGD | Candida Genome Database | http://www.candidagenome.org/cgi-bin/gbrowse/candida_20/ | 200x | |
CGL | Comparative Genomics Library | http://www.yandell-lab.org/cgl/ | 200x | |
The Comprehensive Antibiotic Resistance Database | http://arpcard.mcmaster.ca/ | Yes | 200x | |
cosmoss.org | The Bryophyte Genomics Resource - Physcomitrella patens Annotation | http://www.cosmoss.org | 200x | |
ChromDB | Plant Chromatin Database | http://www.chromdb.org/ | 200x | |
Chromosome 7 Annotation Project | http://www.chr7.org/cgi-bin/gbrowse/gbrowse/chr7_v2 | 200x | ||
CryptoDB | http://cryptodb.org | 200x | ||
CSHLmpd | Mammalian Promoter Database | http://rulai.cshl.edu/cshlmpd/credit.html | 200x | |
Database of Genomic Variants | http://projects.tcag.ca/variation/cgi-bin/gbrowse/hg17 | 200x | ||
DictyBase | http://www.dictybase.org | Yes | 200x | |
DroSpeGe | http://insects.eugenes.org/DroSpeGe/ | 200x | ||
EcoCyc | http://ecocyc.org/ | 200x | ||
Emiliania huxleyi | http://gmod.mbl.edu/emiliania_huxleyi | 200x | ||
Enterocytozoon bieneusi | http://gmod.mbl.edu/perl/site/ebieneusi | 200x | ||
Environmental Sampling Site 396, Fosmid 68 | http://gmod.mbl.edu/perl/site/env396_fosmid68 | 200x | ||
Environmental Sampling Site 396, Fosmid 87 | http://gmod.mbl.edu/perl/site/env396_fosmid87 | 200x | ||
Environmental Sampling Site 396, Fosmids_6_ 56 | http://gmod.mbl.edu/perl/site/env396_fosmids_6_56 | 200x | ||
Environmental Sampling Site Loihi, Red Clone 1 | http://gmod.mbl.edu/perl/site/envloihi_clone1 | 200x | ||
Environmental Sampling Site Loihi, Red Clone 2 | http://gmod.mbl.edu/perl/site/envloihi_clone2 | 200x | ||
Equine Genome | Equus caballus | http://www.equinegenome.org/ | 200x | |
FlyBase | A Database of Drosophila Genes & Genomes | http://www.flybase.org | Yes | 200x |
Fungal Comparitive Genomics | http://fungal.genome.duke.edu/ | 200x | ||
Fungal Telomere Browser | http://genome.kbrin.uky.edu/fungi_tel/browser.html | 200x | ||
Gallus gallus | Gallus gallus SAGE | http://gmod.mbl.edu/perl/site/g_gallus | 200x | |
Gallus Genome Browser | http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chicken | 200x | ||
GeneDB | Pathogen Sequenceing Unit | http://www.genedb.org | Yes | 200x |
giardia14 | http://gmod.mbl.edu/perl/site/giardia14 | 200x | ||
GiardiaDB | http://gmod.mbl.edu/perl/site/giardia?page=intro | 200x | ||
GrainGenes | http://wheat.pw.usda.gov/ | 200x | ||
Gramene | http://www.gramene.org | 200x | ||
HapMap | http://www.hapmap.org/cgi-perl/gbrowse/ | 200x | ||
Human 2q33 | http://t1dbase.cimr.cam.ac.uk/cgi-bin/gbrowse/2q33/ | 200x | ||
Human Genome Segmental Duplication Database | http://projects.tcag.ca/cgi-bin/duplication/dupbrowse/human_b36 | 200x | ||
IVDB | Influenza Virus Database | http://influenza.genomics.org.cn/ | 200x | |
JCVI | J. Craig Venter Institute | http://huref.jcvi.org/browse.html | Yes | 200x |
Leishmania tarentolae RNA editing database | http://gmod.mbl.edu/gb/gbrowse/ltgrna | 200x | ||
LIS | Legume Information System | http://www.comparative-legumes.org/ | 2013 | |
Lepido dB | Lepidoptera database; covers Helicoverpa armigera and Spodoptera frugiperda | http://www.inra.fr/lepidodb | 2012 | |
Livestock Genomics | CSIRO Livestock Industries (LI) livestock genomics; covers bovines and ovines | http://www.livestockgenomics.csiro.au/ | 2013 | |
MAGI | Maize Assembled Genomic Island | http://magi.plantgenomics.iastate.edu/ | 200x | |
Marinobacter aquaeolei | http://gmod.mbl.edu/perl/site/marinobacter_jgi | 200x | ||
Marinobacter aquaeolei FOSMID 38/33. | http://gmod.mbl.edu/perl/site/marinobacter | 200x | ||
MGI | http://www.informatics.jax.org/ | 200x | ||
MSU Rice Genome Browser | http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice | 200x | ||
Non-Human Segmental Duplication Database | http://projects.tcag.ca/xenodup/gbrowse.php | |||
OMAP | Oryza Map Alignment Project | http://www.omap.org/ | 200x | |
Oncorhynchus tshawytscha | Chinook salmon SAGE | http://gmod.mbl.edu/perl/site/salmontrout | 200x | |
OryGenesDB | http://orygenesdb.cirad.fr/ | 200x | ||
Oryza Chromosome 8 | http://map.lab.nig.ac.jp/cgi-bin/gbrowse/Oryza_chr8/ | 200x | ||
OryzaSNP | http://irfgc.irri.org/cgi-bin/gbrowse | 200x | ||
ParameciumDB | http://paramecium.cgm.cnrs-gif.fr/ | Yes | 200x | |
PeanutMap | http://peanutgenetics.tamu.edu/cmap/ | 200x | ||
Philodina roseola | http://gmod.mbl.edu/perl/site/proseola | 200x | ||
PlantsDB | MIPS PlantsDB | http://mips.gsf.de/cgi-bin/proj/plant/gbrowse/synbrowse | 200x | |
PlasmoDB | Plasmodium Genome Resource | http://www.plasmodb.org/ | 200x | |
PopGenIE | The Populus Genome Integrative Explorer | http://www.popgenie.org/ | 200x | |
PossumBase | http://www.possumbase.org.nz/cgi-bin/gbrowse/mondom4/ | 200x | ||
PseudoCAP | Pseudomonas Genome Database | http://v2.pseudomonas.com/whats_new.jsp | 200x | |
PUMAdb | Princeton Microarray Database, Chado | http://puma.princeton.edu/ | 200x | |
RGD | Rat Genome Database | http://rgd.mcw.edu | 200x | |
Rubber Genome Browser | http://bioinfo.ccbusm.edu.my/cgi-bin/gb2/gbrowse/Rubber/ | 200x | ||
Schistosoma mansoni | http://gmod.mbl.edu/perl/site/s_mansonigenome | 200x | ||
Schistosoma mansoni EST | http://gmod.mbl.edu/perl/site/s_mansoniest | 200x | ||
SCRI Plant Bioinformatics Group | http://bioinf.scri.sari.ac.uk/ | Yes | 200x | |
SGD | http://db.yeastgenome.org/cgi-bin/gbrowse/scgenome/ | 200x | ||
S. cerevisiae Proteome Browser | http://db.yeastgenome.org/cgi-bin/gbrowse/scproteome/ | 200x | ||
SGD Lite | http://sgdlite.princeton.edu/ | 200x | ||
SmedGD | Planaria ESTs | http://smedgd.neuro.utah.edu/ | Yes | 200x |
Sol Genomics Network | http://www.sgn.cornell.edu/ | Yes | 200x | |
SoyBase | USDA Soybean Genetics and Genomics Database | http://soybase.org/ | No | 200x |
Soybean GBrowse Database | http://soybeangenome.siu.edu/ | 200x | ||
SpBase | Genome sequence and annotations produced by the Baylor College of Medicine Human Genome Sequencing Center and the sea urchin research community. | http://spbase.org | 200x | |
Synechococcus 4320_2 | http://gmod.mbl.edu/perl/site/syn_4320_2 | 200x | ||
Synechococcus CC9605 | http://gmod.mbl.edu/perl/site/syn_cc9605 | 200x | ||
Synechococcus CC9902 | http://gmod.mbl.edu/perl/site/syn_cc9902 | 200x | ||
Synechococcus RS9916 | http://gmod.mbl.edu/perl/site/syn_rs9916 | 200x | ||
Synechococcus RS9917 | http://gmod.mbl.edu/perl/site/syn_rs9917 | 200x | ||
Synechococcus WH5701 | http://gmod.mbl.edu/perl/site/syn_wh5701 | 200x | ||
Synechococcus WH7805 | http://gmod.mbl.edu/perl/site/syn_wh7805 | 200x | ||
T1DBase | Type 1 Diabetes Database | http://t1dbase.org/cgi-bin/dispatcher.cgi/Welcome/display | 200x | |
TAIR | http://www.arabidopsis.org | 200x | ||
TGD | Tetrahymena Genome Database | http://www.ciliate.org/help/Locus.shtml | 200x | |
TGI | The Gene Index Project | http://biocomp.dfci.harvard.edu/tgi/ | 200x | |
TIGR | The Institute for Genomic Research | http://www.tigr.org | Yes | 200x |
TIGR Medicago BACs | http://www.tigr.org/tigr-scripts/medicago/gbrowse_bacs.pl | 200x | ||
ToxoDB | Toxoplasma gondii database | http://v3-0.toxodb.org/ | 200x | |
TriAnnot BAC Viewer | http://urgi.infobiogen.fr/projects/TriAnnot/GBrowse.php | 200x | ||
Trichomona vaginalis | http://www.uclaaccess.ucla.edu/UCLAACCESS/Web/Faculty.aspx?ri=58 | Yes | 200x | |
TropGENE DB | genetic and genomic information about tropical crops studied by Cirad. | http://tropgenedb.cirad.fr/ | 200x | |
Trypanosoma brucei brucei | http://gmod.mbl.edu/perl/site/t_bruceibrucei02 | 200x | ||
Trypanosoma brucei brucei GenBank Entries | http://gmod.mbl.edu/perl/site/t_bruceigenbank | 200x | ||
Trypanosoma brucei brucei RNA editing database | http://gmod.mbl.edu/gb/gbrowse/grna | 200x | ||
Trypanosoma brucei gambiense | http://gmod.mbl.edu/perl/site/t_bruceigambiense | 200x | ||
Trypanosoma brucei rhodesiense | http://gmod.mbl.edu/perl/site/t_bruceirhodesiense | 200x | ||
Trypanosoma cruzi | http://gmod.mbl.edu/perl/site/t_cruzi | 200x | ||
UNH HCGS Tetraodon Genome Browser | Gbrowse plus GFF | http://hcgs.unh.edu/gbrowse/ | 200x | |
VectorBase | Chado, DAS, Apollo | http://www.vectorbase.org | Yes | 200x |
Vicogenta | Viewer for Comparing Genomes to Arabidopsis | http://nypg.bio.nyu.edu/vicogenta/ | 200x | |
wFleaBase | Daphnia | http://wfleabase.org/ | Yes | 200x |
WormBase | http://www.wormbase.org | 200x | ||
XanthusBase | http://www.xanthusbase.org/ | Yes | 200x | |
Xenbase | http://www.xenbase.org/ | 200x | ||
Xmap | Human X chromosome map for SNP and STR markers used in genetic genealogy and anthropology | http://xmap.ftdna.com/ | No | 2009 |
Yak Genome Database | Yak genome | http://me.lzu.edu.cn/yak/ | 2013 | |
Ymap | Human Y chromosome map for SNP and STR markers used in genetic genealogy and anthropology | http://ymap.ftdna.com/ | No | 2009 |
Microarray data, Chado, H. sapiens | http://genetics.ucla.edu/labs/nelson/ | Yes | 200x | |
http://www.wicell.org | Yes | 200x | ||
Wheat Genome | Wheat | http://www.wheatgenome.info/ | 2013 | |
Human Genome Diversity Project | HGDP @ Pritchard lab, UChicago | http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/ | 2013 | |
eQTL browser | eQTLs identified in recent studies in multiple tissues @ Pritchard lab, UChicago | http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl/ | 2013 | |
Marine Genomics | Multispecies marine organism database | http://marinegenomics.org | Tripal | 2013 |
Hardwood Genomics Project | Hardwood tree spp | http://hardwoodgenomics.org | Tripal | 2013 |
Genome Database for Rosaceae | Rosaceae species | http://rosaceae.org | Tripal | 2013 |
Cacao Genome Database | Cacao | http://cacaogenomedb.org | Tripal | 2013 |
Citrus Genome Database | Citrus | http://citrusgenomedb.org | Tripal | 2013 |
Cool Season Food Legume Database | Cool season legumes, e.g. pea, lentil, chickpea, fava beans, etc. | http://gabcsfl.org | Tripal | 2013 |
Fagaceae Genomics Web | Fagaceae spp, including oak, beech, chestnut, etc. | http://fagaceae.org | Tripal | 2013 |
Cottongen | added 2013 | http://www.cottongen.org/ | Tripal | 2013 |
Banana Genome Hub | added 2013 | http://banana-genome.cirad.fr/ | Tripal | 2013 |
KnowPulse: Pulse Crop Genomics & Breeding | Chickpea, lentil, common bean, pea | http://knowpulse2.usask.ca/portal/ | Tripal | 2013 |
Genomic DB for Vaccinium | Blueberry, cranberry, lingonberry, other Vaccinium spp. | http://www.vaccinium.org/ | Tripal | 2013 |
GBrowse Users
This is a list of confirmed GBrowse users as of April 2004.
- Agricultural Biotechnology Center, Hungary
- AphidBase
- 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
- Family Tree DNA, Genealogy by Genetics Ltd.
- 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
- NHGRI, NIH
- 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
- SoyBase
- St. Jude Children's Research Hospital, Memphis
- Stowers Institute for Medical Research
- Texas A&M (multiple labs)
- Texas Biomedical Research Institute
- The Institute for Genome Research
- 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
- Xenbase
- deVGen, Belgium