GMOD Users

From GMOD
Revision as of 03:44, 27 February 2013 by Girlwithglasses (Talk | contribs)

Jump to: navigation, search

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
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
Eimeria transcript database Annotated transcripts of protozoan parasites of the genus Eimeria http://www.coccidia.icb.usp.br/eimeriatdb/
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
AphidBase Pea aphid genome http://www.aphidbase.com/ Yes
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/
The Comprehensive Antibiotic Resistance Database http://arpcard.mcmaster.ca/ Yes
cosmoss.org The Bryophyte Genomics Resource - Physcomitrella patens Annotation http://www.cosmoss.org
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
Equine Genome Equus caballus http://www.equinegenome.org/
FlyBase A Database of Drosophila Genes & Genomes 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/
JCVI J. Craig Venter Institute http://huref.jcvi.org/browse.html Yes
Leishmania tarentolae RNA editing database http://gmod.mbl.edu/gb/gbrowse/ltgrna
LIS Legume Information System http://www.comparative-legumes.org/
Lepido dB Lepidoptera database [2012]

Covers Helicoverpa armigera and Spodoptera frugiperda

http://www.inra.fr/lepidodb
Livestock Genomics CSIRO Livestock Industries (LI) livestock genomics

Covers bovines and ovines

http://www.livestockgenomics.csiro.au/
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/
MSU Rice Genome Browser http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice
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/
OryzaSNP http://irfgc.irri.org/cgi-bin/gbrowse
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/
PopGenIE The Populus Genome Integrative Explorer http://www.popgenie.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
Rubber Genome Browser http://bioinfo.ccbusm.edu.my/cgi-bin/gb2/gbrowse/Rubber/
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/
SmedGD Planaria ESTs http://smedgd.neuro.utah.edu/ Yes
Sol Genomics Network http://www.sgn.cornell.edu/ Yes
SoyBase USDA Soybean Genetics and Genomics Database http://soybase.org/ No
Soybean GBrowse Database http://soybeangenome.siu.edu/
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
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
ToxoDB Toxoplasma gondii database http://v3-0.toxodb.org/
TriAnnot BAC Viewer http://urgi.infobiogen.fr/projects/TriAnnot/GBrowse.php
Trichomona vaginalis http://www.uclaaccess.ucla.edu/UCLAACCESS/Web/Faculty.aspx?ri=58 Yes
TropGENE DB genetic and genomic information about tropical crops studied by Cirad. http://tropgenedb.cirad.fr/
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/
Xmap Human X chromosome map for SNP and STR markers used in genetic genealogy and anthropology (public available on 3/2/2009) http://xmap.ftdna.com/ No
Yak Genome Database [2012] http://me.lzu.edu.cn/yak
Ymap Human Y chromosome map for SNP and STR markers used in genetic genealogy and anthropology (public available on 3/2/2009) http://ymap.ftdna.com/ No
Microarray data, Chado, H. sapiens http://genetics.ucla.edu/labs/nelson/ Yes
http://www.wicell.org Yes
Wheat Genome Wheat http://www.wheatgenome.info/
Human Genome Diversity Project HGDP @ Pritchard lab, UChicago http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/
eQTL browser eQTLs identified in recent studies in multiple tissues @ Pritchard lab, UChicago http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl/

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
Retrieved from "http://gmod.org/mediawiki/index.php?title=GMOD_Users&oldid=23171"