Difference between revisions of "GMOD Users"

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

Revision as of 23:10, 28 February 2013

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
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