GMOD Users

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GMOD Users

The following databases use GBrowse or Chado or some other popular component of GMOD.

Name Description Location Contacts Email 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 Hilary Morrison
ApiDB http://apidb.org/apidb/
ATIDB Arabidopsis http://atidb.org
Aureococcus http://gmod.mbl.edu/perl/site/aureococcus Sonya Dyhrman, Andrew McArthur
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 Christine Elsik
BeetleBase Gbrowse UI http://www.bioinformatics.ksu.edu/BeetleBase/ Susan Brown sjbrown@ksu.edu Yes
BGD Bovine Genome Database http://bovinegenome.org/ Christine Elsik kchilds@neo.tamu.edu
BioHealthBase BioDefense Public Health Database http://www.biohealthbase.org/GSearch/ Chris Larsen
Blochmannia pennsylvanicus http://gmod.mbl.edu/perl/site/blochmannia06 Jennifer Wernegreen
Bovine QTL Viewer http://bovineqtl.tamu.edu
Brachionus plicatilis A http://gmod.mbl.edu/perl/site/bplicatilisa David Mark Welch
Brachionus plicatilis B http://gmod.mbl.edu/perl/site/bplicatilisb David Mark Welch
Cattle EST Gene Family Database http://racerx00.tamu.edu/cgi-test/searchCattleDatabase.html Christine Elsik
CGD Candida Genome Database http://hypha.stanford.edu/
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 Steve Scherer
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 Steve Scherer
DictyBase http://www.dictybase.org Yes
DroSpeGe http://insects.eugenes.org/DroSpeGe/
EcoCyc http://ecocyc.org/
Emiliania huxleyi http://gmod.mbl.edu/emiliania_huxleyi Sonya Dyhrman, Andrew McArthur
Enterocytozoon bieneusi http://gmod.mbl.edu/perl/site/ebieneusi Hilary Morrison
Environmental Sampling Site 396, Fosmid 68 http://gmod.mbl.edu/perl/site/env396_fosmid68 Julie Huber
Environmental Sampling Site 396, Fosmid 87 http://gmod.mbl.edu/perl/site/env396_fosmid87 Julie Huber
Environmental Sampling Site 396, Fosmids_6_ 56 http://gmod.mbl.edu/perl/site/env396_fosmids_6_56 Julie Huber
Environmental Sampling Site Loihi, Red Clone 1 http://gmod.mbl.edu/perl/site/envloihi_clone1 Ashita Dhillon
Environmental Sampling Site Loihi, Red Clone 2 http://gmod.mbl.edu/perl/site/envloihi_clone2 Ashita Dhillon
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 Sean Kennedy, Andrew McArthur
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/ Lincoln Stein
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 Steve Scherer
IVDB Influenza Virus Database http://influenza.genomics.org.cn/
Leishmania tarentolae RNA editing database http://gmod.mbl.edu/gb/gbrowse/ltgrna Torsten Ochsenreiter
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 Susan Huse
Marinobacter aquaeolei FOSMID 38/33. http://gmod.mbl.edu/perl/site/marinobacter Ashita Dhillon
MGI http://www.informatics.jax.org/
Non-Human Segmental Duplication Database http://projects.tcag.ca/xenodup/gbrowse.php Steve Scherer
OMAP Oryza Map Alignment Project http://www.omap.org/ Rod Wing rwing@genome.arizona.edu
Oncorhynchus tshawytscha Chinook salmon SAGE http://gmod.mbl.edu/perl/site/salmontrout Jeremiah Bernier, Andrew McArthur
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/ mburow@tamu.edu
Philodina roseola http://gmod.mbl.edu/perl/site/proseola David Mark Welch
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 pseudocap-mail@sfu.ca
PUMAdb Princeton Microarray Database, Chado http://puma.princeton.edu/ array@genomics.princeton.edu
RGD Rat Genome Database http://rgd.mcw.edu
Schistosoma mansoni http://gmod.mbl.edu/perl/site/s_mansonigenome Andrew McArthur
Schistosoma mansoni EST http://gmod.mbl.edu/perl/site/s_mansoniest Andrew McArthur
SGD http://www.yeastgenome.org Mike Cherry
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/
SpBase
Synechococcus 4320_2 http://gmod.mbl.edu/perl/site/syn_4320_2 Anton Post
Synechococcus CC9605 http://gmod.mbl.edu/perl/site/syn_cc9605 Anton Post
Synechococcus CC9902 http://gmod.mbl.edu/perl/site/syn_cc9902 Anton Post
Synechococcus RS9916 http://gmod.mbl.edu/perl/site/syn_rs9916 Anton Post
Synechococcus RS9917 http://gmod.mbl.edu/perl/site/syn_rs9917 Anton Post
Synechococcus WH5701 http://gmod.mbl.edu/perl/site/syn_wh5701 Anton Post
Synechococcus WH7805 http://gmod.mbl.edu/perl/site/syn_wh7805 Anton Post
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 Andrew McArthur
Trypanosoma brucei brucei GenBank Entries http://gmod.mbl.edu/perl/site/t_bruceigenbank Andrew McArthur
Trypanosoma brucei brucei RNA editing database http://gmod.mbl.edu/gb/gbrowse/grna Torsten Ochsenreiter
Trypanosoma brucei gambiense http://gmod.mbl.edu/perl/site/t_bruceigambiense Michael Cipriano
Trypanosoma brucei rhodesiense http://gmod.mbl.edu/perl/site/t_bruceirhodesiense Andrew McArthur
Trypanosoma cruzi http://gmod.mbl.edu/perl/site/t_cruzi Michael Cipriano
UNH HCGS Tetraodon Genome Browser Gbrowse plus GFF http://hcgs.unh.edu/gbrowse/ Tom Koccher
VectorBase Chado, DAS, Apollo http://www.vectorbase.org Yes
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 Patricia Johnson, UCLA Yes
Microarray data, Chado, H. sapiens http://genetics.ucla.edu/labs/nelson/ Stan Nelson, UCLA Yes
http://www.wicell.org Wicell Research Institute Yes
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