Difference between revisions of "GMOD Users"

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m (Editing list of GMOD users)
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|-
 
|-
 
| http://arpcard.mcmaster.ca/ || The Comprehensive Antibiotic Resistance Database || Bioinformatics database of resistance genes, their products and associated phenotypes. || Yes || 2013
 
| http://arpcard.mcmaster.ca/ || The Comprehensive Antibiotic Resistance Database || Bioinformatics database of resistance genes, their products and associated phenotypes. || Yes || 2013
 +
|-
 +
| http://aspergillusgenome.org/ || AspGD || Aspergillus || GBrowse, Sybil || 2013
 
|-
 
|-
 
| http://asrp.danforthcenter.org/ || Arabidopsis Small RNA Project (ASRP) || Arabidopsis || JBrowse || 2013
 
| http://asrp.danforthcenter.org/ || Arabidopsis Small RNA Project (ASRP) || Arabidopsis || JBrowse || 2013
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| http://beetlebase.org/ || BeetleBase || ''Tribolium castaneum'' || Gbrowse, JBrowse, Chado || 2013
 
| http://beetlebase.org/ || BeetleBase || ''Tribolium castaneum'' || Gbrowse, JBrowse, Chado || 2013
 
|-
 
|-
−
| http://compbio.dfci.harvard.edu/tgi/ || TGI || The Gene Index Project: uses ESTs and gene sequences to predict genes and variants || GBrowse || 2013
+
| http://bioinf.gen.tcd.ie/jbrowse/SL1344/ || Salmonella || transcriptional map of S. Typhimurium || JBrowse || 2013
 
|-
 
|-
 
| http://bioinf.hutton.ac.uk/public/ || SCRI Plant Bioinformatics Group ||  || Yes || 200x
 
| http://bioinf.hutton.ac.uk/public/ || SCRI Plant Bioinformatics Group ||  || Yes || 200x
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|-
 
|-
 
| http://bioinfo.ccbusm.edu.my/cgi-bin/gb2/gbrowse/Rubber/ || Rubber Genome Browser || (not accessible to public - Mar 2013) ||  || 2013
 
| http://bioinfo.ccbusm.edu.my/cgi-bin/gb2/gbrowse/Rubber/ || Rubber Genome Browser || (not accessible to public - Mar 2013) ||  || 2013
 +
|-
 +
| http://bioinformatics.ai.sri.com/ptools/ || [[Pathway Tools]] || || Home of Pathway Tools || 2013
 
|-
 
|-
 
| http://bovinegenome.org/ || BGD || Bovine Genome Database ||  || 200x
 
| http://bovinegenome.org/ || BGD || Bovine Genome Database ||  || 200x
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|-
 
|-
 
| http://www.coccidia.icb.usp.br/eimeriatdb/ || ''Eimeria'' transcript database || Annotated transcripts of protozoan parasites of the genus Eimeria ||  || 2013
 
| http://www.coccidia.icb.usp.br/eimeriatdb/ || ''Eimeria'' transcript database || Annotated transcripts of protozoan parasites of the genus Eimeria ||  || 2013
 +
|-
 +
| http://compbio.dfci.harvard.edu/tgi/ || TGI || The Gene Index Project: uses ESTs and gene sequences to predict genes and variants || GBrowse || 2013
 
|-
 
|-
 
| http://www.comparative-legumes.org/ || LIS || Legume Information System || CMap || 2013
 
| http://www.comparative-legumes.org/ || LIS || Legume Information System || CMap || 2013
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| http://www.cottongen.org/ || Cottongen ||  || Tripal || 2013
 
| http://www.cottongen.org/ || Cottongen ||  || Tripal || 2013
 
|-
 
|-
−
| http://crfb.univ-mrs.fr/ciona-bin/gbrowse/intestinalis/ || ANISEED || Ascidian Network for In Situ Expression and Embryological Data || || 200x
+
| http://aniseed-ibdm.univ-mrs.fr/ || ANISEED || Ascidian Network for In Situ Expression and Embryological Data || GBrowse || 2013
 
|-
 
|-
 
| http://cryptodb.org || CryptoDB || Cryptosporidium (part of EupathDB) || GBrowse, Cyc|| 2013
 
| http://cryptodb.org || CryptoDB || Cryptosporidium (part of EupathDB) || GBrowse, Cyc|| 2013
 +
|-
 +
| http://db-mml.sjtu.edu.cn/ThioFinder/search.html || ThioBase || A database of thiopeptides featured in genetics and chemistry || GBrowse_syn || 2013
 
|-
 
|-
 
| http://diagcomputing.org/resources/software.php || Data-Intensive Academic Grid || Provides a VM/cloud image of bioinf. software || JBrowse, BioMart, Ergatis, etc. || 2013
 
| http://diagcomputing.org/resources/software.php || Data-Intensive Academic Grid || Provides a VM/cloud image of bioinf. software || JBrowse, BioMart, Ergatis, etc. || 2013
 
|-
 
|-
−
| http://www.dictybase.org || [[:Category:DictyBase|DictyBase]] ||  || Yes || 200x
+
| http://www.dictybase.org || [[:Category:DictyBase|DictyBase]] ||  || Yes || 2013
 +
|-
 +
| http://ecobrowser.biosino.org || EcoBrowser || E. coli transcriptome || JBrowse || 2013
 
|-
 
|-
 
| http://ecocyc.org/ || EcoCyc ||  ||  || 2013
 
| http://ecocyc.org/ || EcoCyc ||  ||  || 2013
 +
|-
 +
| http://ecoliwiki.net || EcoliWiki || E. coli || || 2013
 
|-
 
|-
 
| http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl/ || eQTL browser || eQTLs identified in recent studies in multiple tissues @ [http://pritch.bsd.uchicago.edu/ Pritchard lab, UChicago] || || 2013
 
| http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl/ || eQTL browser || eQTLs identified in recent studies in multiple tissues @ [http://pritch.bsd.uchicago.edu/ Pritchard lab, UChicago] || || 2013
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|-
 
|-
 
| http://www.flybase.org || [[:Category:FlyBase|FlyBase]] || A Database of Drosophila Genes & Genomes || Yes || 2013
 
| http://www.flybase.org || [[:Category:FlyBase|FlyBase]] || A Database of Drosophila Genes & Genomes || Yes || 2013
 +
|-
 +
| http://fungalgenomes.org/ || Fungal Genomes || Fungal Genomics Resources || || 2013
 
|-
 
|-
 
| http://fungidb.org/ || FungiDB || Fungal Genomics Resources || || 2013
 
| http://fungidb.org/ || FungiDB || Fungal Genomics Resources || || 2013
 
|-
 
|-
−
| http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/A_fumigatus_tigr_tel_100k || A. fumigatus TIGR/Sanger Assembly ||  ||  || 200x
+
| http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/A_fumigatus_tigr_tel_100k || A. fumigatus TIGR/Sanger Assembly ||  ||  || 2013
 +
|-
 +
| http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/S_nodorum_broad_tel_100k || S. nodorum Fungal Telomere Browser ||  ||  || 2013
 
|-
 
|-
 
| http://gabcsfl.org || Cool Season Food Legume Database || Cool season legumes, e.g. pea, lentil, chickpea, fava beans, etc. || Tripal || 2013
 
| http://gabcsfl.org || Cool Season Food Legume Database || Cool season legumes, e.g. pea, lentil, chickpea, fava beans, etc. || Tripal || 2013
 
|-
 
|-
−
| http://www.genedb.org || GeneDB || Pathogen Sequencing Unit || Chado, JBrowse || 200x
+
| http://gbrowse.jcvi.org/gbrowse/ || JCVI || J. Craig Venter Institute; offers numerous species || || 2013
 +
|-
 +
| https://gdoc.georgetown.edu/gdoc/ || G-DOC || Systems medicine platform for personalized oncology || JBrowse || 2013
 +
|-
 +
| http://www.genedb.org || GeneDB || Pathogen Sequencing Unit || Chado, JBrowse || 2013
 +
|-
 +
| http://www.generationcp.org/ || Generation Challenge Programme ||
 
|-
 
|-
 
| http://genomes.sapac.edu.au/bovineqtl/ || Bovine QTL Viewer ||  ||  || 2013
 
| http://genomes.sapac.edu.au/bovineqtl/ || Bovine QTL Viewer ||  ||  || 2013
 
|-
 
|-
−
| http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/S_nodorum_broad_tel_100k?name=telomere_1 || S. nodorum Fungal Telomere Browser || || || 200x
+
| http://www.genomesunzipped.org/jbrowse/ || Genomes Unzipped || Human -- personal genomic data made public || JBrowse || 2013
 
|-  
 
|-  
 
| http://www.genoscope.cns.fr/spip/Ressources-bioinformatiques-du.html || Genoscope || Multiple organisms || GBrowse || 2013
 
| http://www.genoscope.cns.fr/spip/Ressources-bioinformatiques-du.html || Genoscope || Multiple organisms || GBrowse || 2013
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|-
 
|-
 
| http://www.gramene.org || [[:Category:Gramene|Gramene]] ||  ||  || 2013
 
| http://www.gramene.org || [[:Category:Gramene|Gramene]] ||  ||  || 2013
 +
|-
 +
| http://green.dna.affrc.go.jp/Og/ || AfRicA DB || African Rice Annotation DataBase || GBrowse || 2013
 
|-
 
|-
 
| http://hapmap.ncbi.nlm.nih.gov/index.html.en || HapMap ||  ||  || 2013
 
| http://hapmap.ncbi.nlm.nih.gov/index.html.en || HapMap ||  ||  || 2013
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|-
 
|-
 
| http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/ || Human Genome Diversity Project || HGDP @ [http://pritch.bsd.uchicago.edu/ Pritchard lab, UChicago] || || 2013
 
| http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/ || Human Genome Diversity Project || HGDP @ [http://pritch.bsd.uchicago.edu/ Pritchard lab, UChicago] || || 2013
−
|-
 
−
| http://gbrowse.jcvi.org/gbrowse/ || JCVI || J. Craig Venter Institute; offers numerous species || || 2013
 
 
|-
 
|-
 
| http://hymenopteragenome.org/beebase/ || BeeBase || The secret life of bees || JBrowse || 2013
 
| http://hymenopteragenome.org/beebase/ || BeeBase || The secret life of bees || JBrowse || 2013
 +
|-
 +
| http://hymenopteragenome.org/ant_genomes/ || Ant Genomes Portal || Ants || GBrowse || 2013
 +
|-
 +
| http://hymenopteragenome.org/nasonia/ || NasoniaBase || Nasonia wasp || GBrowse || 2013
 
|-
 
|-
 
| http://icemangenome.net/ || Ice Man Genome || The genome of Ötzi the Iceman || JBrowse || 2013
 
| http://icemangenome.net/ || Ice Man Genome || The genome of Ötzi the Iceman || JBrowse || 2013
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|-
 
|-
 
| http://irfgc.irri.org/cgi-bin/gbrowse || OryzaSNP ||  ||  || 200x
 
| http://irfgc.irri.org/cgi-bin/gbrowse || OryzaSNP ||  ||  || 200x
 +
|-
 +
| http://iubio.bio.indiana.edu/ || IUBio Archive || Software and data from Indiana University; includes numerous resources, such as euGenes, DroSpeGe, wFleaBase, etc. || Argos || 2013
 
|-
 
|-
 
| http://www.jcvi.org || TIGR || The Institute for Genomic Research || Yes || 200x
 
| http://www.jcvi.org || TIGR || The Institute for Genomic Research || Yes || 200x
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|-
 
|-
 
| http://krithgenomics.drupalgardens.com/ || K-RITH-Hopkins Genomics Web Portal ||  || JBrowse || 2013
 
| http://krithgenomics.drupalgardens.com/ || K-RITH-Hopkins Genomics Web Portal ||  || JBrowse || 2013
 +
|-
 +
| http://lgd.abcc.ncifcrf.gov/cgi-bin/gbrowse/cat/ || GARFIELD || Genome Annotation Resource Field Felis catus || GBrowse || 2013
 
|-
 
|-
 
| http://www.livestockgenomics.csiro.au/ || Livestock Genomics || CSIRO Livestock Industries (LI) livestock genomics; covers bovines and ovines || || 2013
 
| http://www.livestockgenomics.csiro.au/ || Livestock Genomics || CSIRO Livestock Industries (LI) livestock genomics; covers bovines and ovines || || 2013
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|-
 
|-
 
| http://www.medicinalgenomics.com/the-jane-ome/ || The Jane-Ome || Cannabis Genome Project, Medicinal Marijuana || JBrowse || 2013
 
| http://www.medicinalgenomics.com/the-jane-ome/ || The Jane-Ome || Cannabis Genome Project, Medicinal Marijuana || JBrowse || 2013
 +
|-
 +
| http://mg.dna.affrc.go.jp/ || MgEST DB || Magnaporthe grisea ESTs ||  GBrowse || 2013
 +
|-
 +
| http://microb215.med.upenn.edu/gb2/gbrowse/phage_metagenomics/ || Phage metagenomics || || GBrowse || 2013
 
|-
 
|-
 
| http://microsporidiadb.org || MicrosporidiaDB || Microsporidia (part of EupathDB) || || 2013
 
| http://microsporidiadb.org || MicrosporidiaDB || Microsporidia (part of EupathDB) || || 2013
 
|-
 
|-
 
| http://mips.helmholtz-muenchen.de/plant/triticeae/index.jsp || MIPS Triticeae genomes database || Barley, wheat, rye || || 2013
 
| http://mips.helmholtz-muenchen.de/plant/triticeae/index.jsp || MIPS Triticeae genomes database || Barley, wheat, rye || || 2013
 +
|-
 +
| http://nabic.rda.go.kr/ || NABIC RDA || Various plant and animal genomes || GBrowse_syn, GBrowse || 2013
 
|-
 
|-
 
| http://nypg.bio.nyu.edu/vicogenta/ || Vicogenta || Viewer for Comparing Genomes to Arabidopsis ||  || 200x
 
| http://nypg.bio.nyu.edu/vicogenta/ || Vicogenta || Viewer for Comparing Genomes to Arabidopsis ||  || 200x
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|-
 
|-
 
| http://www.omap.org/ || OMAP || Oryza Map Alignment Project || || 200x
 
| http://www.omap.org/ || OMAP || Oryza Map Alignment Project || || 200x
 +
|-
 +
| http://www.opossumbase.org/ || OpossumBase || Monodelphis domestica Genomic Resources Database || GBrowse, JBrowse || 2013
 
|-
 
|-
 
| http://orygenesdb.cirad.fr/ || OryGenesDB ||  ||  || 200x
 
| http://orygenesdb.cirad.fr/ || OryGenesDB ||  ||  || 200x
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-->
 
-->
 
|-
 
|-
−
| http://pseudomonas.com/whats_new.jsp || PseudoCAP || Pseudomonas Genome Database ||  || 200x
+
| http://pseudomonas.com/ || PseudoCAP || Pseudomonas Genome Database ||  || 200x
 
|-
 
|-
 
| http://puma.princeton.edu/ || PUMAdb || Princeton Microarray Database, Chado ||  || 200x
 
| http://puma.princeton.edu/ || PUMAdb || Princeton Microarray Database, Chado ||  || 200x
 +
|-
 +
| http://qtaro.abr.affrc.go.jp/ || QTARO || QTL Annotation Rice Online || GBrowse || 2013
 +
|-
 +
| http://rapdb.dna.affrc.go.jp/ || Rice Annotation Project DB || || GBrowse || 2013
 +
|-
 +
| http://research.nhgri.nih.gov/mnemiopsis/ || Mnemiopsis Genome Project || The ctenophore '''Mnemiopsis leidyi''' || JBrowse || 2013
 
|-
 
|-
 
| http://rgd.mcw.edu || [[:Category:RGD|RGD]] || Rat Genome Database ||  || 200x
 
| http://rgd.mcw.edu || [[:Category:RGD|RGD]] || Rat Genome Database ||  || 200x
 
|-
 
|-
 
| http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice || MSU Rice Genome Browser ||  ||  || 2013
 
| http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice || MSU Rice Genome Browser ||  ||  || 2013
 +
|-
 +
| http://rnaspace.org/ || RNAspace || an integrated environment for non-coding RNA annotation || JBrowse || 2013
 
|-
 
|-
 
| http://www.rosaceae.org || Genome Database for Rosaceae || Rosaceae species || Tripal || 2013
 
| http://www.rosaceae.org || Genome Database for Rosaceae || Rosaceae species || Tripal || 2013
 
|-
 
|-
−
| http://rulai.cshl.edu/cshlmpd/credit.html || CSHLmpd || Mammalian Promoter Database ||  || 200x
+
| http://rulai.cshl.edu/cshlmpd/credit.html || CSHLmpd || Mammalian Promoter Database ||  || 2013
 
|-
 
|-
 
| http://sgdlite.princeton.edu/ || SGD Lite ||  ||  || 200x
 
| http://sgdlite.princeton.edu/ || SGD Lite ||  ||  || 200x
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| http://www.shigen.nig.ac.jp/barley/ || BarleyDB || Barley! || GBrowse, CMap || 2013
 
| http://www.shigen.nig.ac.jp/barley/ || BarleyDB || Barley! || GBrowse, CMap || 2013
 
|-
 
|-
−
| http://smedgd.neuro.utah.edu/ || SmedGD || Planaria ESTs || Yes || 200x
+
| http://smedgd.neuro.utah.edu/ || SmedGD || Planaria ESTs || Yes || 2013
 
|-
 
|-
−
| http://solgenomics.net/ || [[:Category:SGN|Sol Genomics Network]] ||  || Yes || 200x
+
| http://solgenomics.net/ || [[:Category:SGN|Sol Genomics Network]] ||  || Yes || 2013
 
|-
 
|-
 
| http://soybase.org/ || SoyBase || USDA Soybean Genetics and Genomics Database || No || 200x
 
| http://soybase.org/ || SoyBase || USDA Soybean Genetics and Genomics Database || No || 200x
 +
|-
 +
| http://soybeangenome.siu.edu/ || Soybean Gbrowse Database || || GBrowse || 2013
 
|-
 
|-
 
| http://spbase.org || 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. || GBrowse, BioMart, Textpresso || 2013
 
| http://spbase.org || 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. || GBrowse, BioMart, Textpresso || 2013
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| http://www.wormbase.org || [[:Category:WormBase|WormBase]] ||  ||  || 2013
 
| http://www.wormbase.org || [[:Category:WormBase|WormBase]] ||  ||  || 2013
 
|-
 
|-
−
| http://www.xanthusbase.org/ || XanthusBase ||  || Yes || 2013
+
| http://www.xenbase.org/ || Xenbase || Xenopus ||  || 2013
−
|-
+
−
| http://www.xenbase.org/ || Xenbase || ||  || 2013
+
 
|-
 
|-
 
| http://xmap.ftdna.com/ || Xmap || Human X chromosome map for SNP and STR markers used in genetic genealogy and anthropology || No || 2013
 
| http://xmap.ftdna.com/ || Xmap || Human X chromosome map for SNP and STR markers used in genetic genealogy and anthropology || No || 2013
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|-
 
|-
 
| http://ymap.ftdna.com/ || Ymap || Human Y chromosome map for SNP and STR markers used in genetic genealogy and anthropology || No || 2013
 
| http://ymap.ftdna.com/ || Ymap || Human Y chromosome map for SNP and STR markers used in genetic genealogy and anthropology || No || 2013
 +
|-
 +
| http://zfin.org/ || ZFIN || Zebrafish, '''Danio rerio''' || GBrowse || 2013
 
|}
 
|}
  
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* Xenbase
 
* Xenbase
 
* deVGen, Belgium
 
* deVGen, Belgium
−
 
−
[[Category:Chado]]
 
−
[[Category:GBrowse]]
 
−
[[Category:GMOD Community]]
 

Revision as of 01:03, 8 March 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
http://agripestbase.org Agripestbase Agricultural pests 2013
http://agripestbase.org/hessianfly Hessian fly part of Agripestbase 2013
http://agripestbase.org/manduca Manduca sexta part of Agripestbase 2013
http://amoebadb.org AmoebaDB Amoeba (part of EupathDB) 2013
http://animalgenome.org National Animal Genome Research Program Animal genomes! GBrowse 2013
http://www.aphidbase.com/ AphidBase Pea aphid genome Apollo, Chado, Galaxy, GBrowse, Cycs 2013
http://www.arabidopsis.org TAIR 2013
http://arpcard.mcmaster.ca/ The Comprehensive Antibiotic Resistance Database Bioinformatics database of resistance genes, their products and associated phenotypes. Yes 2013
http://aspergillusgenome.org/ AspGD Aspergillus GBrowse, Sybil 2013
http://asrp.danforthcenter.org/ Arabidopsis Small RNA Project (ASRP) Arabidopsis JBrowse 2013
http://atidb.org ATIDB Arabidopsis 200x
http://banana-genome.cirad.fr/ Banana Genome Hub Tripal 2013
http://beetlebase.org/ BeetleBase Tribolium castaneum Gbrowse, JBrowse, Chado 2013
http://bioinf.gen.tcd.ie/jbrowse/SL1344/ Salmonella transcriptional map of S. Typhimurium JBrowse 2013
http://bioinf.hutton.ac.uk/public/ SCRI Plant Bioinformatics Group Yes 200x
http://bioinfo.cau.edu.cn/ProFITS/index.php ProFITS Protein Families Involved in the Transduction of Signalling (Maize) JBrowse, GBrowse 2013
http://bioinfo.ccbusm.edu.my/cgi-bin/gb2/gbrowse/Rubber/ Rubber Genome Browser (not accessible to public - Mar 2013) 2013
http://bioinformatics.ai.sri.com/ptools/ Pathway Tools Home of Pathway Tools 2013
http://bovinegenome.org/ BGD Bovine Genome Database 200x
http://www.brachybase.org/ Brachypodium JBrowse 2013
http://butterflybase.ice.mpg.de/ ButterflyBase (part of InsectaCentral) Butterflies and moths GBrowse 2013
http://www.cacaogenomedb.org Cacao Genome Database Cacao Tripal 2013
http://www.candidagenome.org/cgi-bin/gbrowse/candida_20/ CGD Candida Genome Database 200x
http://www.chr7.org/cgi-bin/gbrowse/gbrowse/chr7_v2/ Chromosome 7 Annotation Project 200x
http://www.chromdb.org/ ChromDB Plant Chromatin Database 200x
http://www.ciliate.org/ TGD Tetrahymena Genome Database 2013
http://www.citrusgenomedb.org Citrus Genome Database Citrus Tripal 2013
http://citrusgreening.org/ Citrus Greening pathogens causing citrus greening (Huanglongbing or HLB), esp. Liberibacter 2013
http://www.coccidia.icb.usp.br/eimeriatdb/ Eimeria transcript database Annotated transcripts of protozoan parasites of the genus Eimeria 2013
http://compbio.dfci.harvard.edu/tgi/ TGI The Gene Index Project: uses ESTs and gene sequences to predict genes and variants GBrowse 2013
http://www.comparative-legumes.org/ LIS Legume Information System CMap 2013
http://www.cosmoss.org cosmoss.org The Bryophyte Genomics Resource - Physcomitrella patens Annotation 200x
http://www.cottongen.org/ Cottongen Tripal 2013
http://aniseed-ibdm.univ-mrs.fr/ ANISEED Ascidian Network for In Situ Expression and Embryological Data GBrowse 2013
http://cryptodb.org CryptoDB Cryptosporidium (part of EupathDB) GBrowse, Cyc 2013
http://db-mml.sjtu.edu.cn/ThioFinder/search.html ThioBase A database of thiopeptides featured in genetics and chemistry GBrowse_syn 2013
http://diagcomputing.org/resources/software.php Data-Intensive Academic Grid Provides a VM/cloud image of bioinf. software JBrowse, BioMart, Ergatis, etc. 2013
http://www.dictybase.org DictyBase Yes 2013
http://ecobrowser.biosino.org EcoBrowser E. coli transcriptome JBrowse 2013
http://ecocyc.org/ EcoCyc 2013
http://ecoliwiki.net EcoliWiki E. coli 2013
http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl/ eQTL browser eQTLs identified in recent studies in multiple tissues @ Pritchard lab, UChicago 2013
http://www.equinegenome.org/ Equine Genome Equus caballus 200x
http://eupathdb.org EupathDB Eukaryotic pathogens, including Babesia, Crithidia, Cryptosporidium, Edhazardia, Eimeria, Encephalitozoon, Endotrypanum, Entamoeba, Enterocytozoon, Giardia, Gregarina, Hamiltosporidium, Leishmania, Nematocida, Neospora, Nosema, Plasmodium, Theileria, Toxoplasma, Trichomonas, Trypanosoma, and Vivraia 2013
http://fagaceae.org Fagaceae Genomics Web Fagaceae spp, including oak, beech, chestnut, etc. Tripal 2013
http://www.flybase.org FlyBase A Database of Drosophila Genes & Genomes Yes 2013
http://fungalgenomes.org/ Fungal Genomes Fungal Genomics Resources 2013
http://fungidb.org/ FungiDB Fungal Genomics Resources 2013
http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/A_fumigatus_tigr_tel_100k A. fumigatus TIGR/Sanger Assembly 2013
http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/S_nodorum_broad_tel_100k S. nodorum Fungal Telomere Browser 2013
http://gabcsfl.org Cool Season Food Legume Database Cool season legumes, e.g. pea, lentil, chickpea, fava beans, etc. Tripal 2013
http://gbrowse.jcvi.org/gbrowse/ JCVI J. Craig Venter Institute; offers numerous species 2013
https://gdoc.georgetown.edu/gdoc/ G-DOC Systems medicine platform for personalized oncology JBrowse 2013
http://www.genedb.org GeneDB Pathogen Sequencing Unit Chado, JBrowse 2013
http://www.generationcp.org/ Generation Challenge Programme
http://genomes.sapac.edu.au/bovineqtl/ Bovine QTL Viewer 2013
http://www.genomesunzipped.org/jbrowse/ Genomes Unzipped Human -- personal genomic data made public JBrowse 2013
http://www.genoscope.cns.fr/spip/Ressources-bioinformatiques-du.html Genoscope Multiple organisms GBrowse 2013
http://genexpdb.ou.edu/main/ E. coli GenExpDB E. coli Gene Expression Database JBrowse 2013
http://giardiadb.org GiardiaDB Giardia (part of EupathDB) 2013
http://github.com/capsid CaPSID Computational Pathogen Sequence IDentification - open source platform for pathogen sequence identification JBrowse 2013
http://gmod.mbl.edu/ JBPC Generic Model Organism Database servers Huge set of GMOD/GBrowse resources covering many different species 2013
http://www.gramene.org Gramene 2013
http://green.dna.affrc.go.jp/Og/ AfRicA DB African Rice Annotation DataBase GBrowse 2013
http://hapmap.ncbi.nlm.nih.gov/index.html.en HapMap 2013
http://www.hardwoodgenomics.org Hardwood Genomics Project Hardwood tree spp Tripal 2013
http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/ Human Genome Diversity Project HGDP @ Pritchard lab, UChicago 2013
http://hymenopteragenome.org/beebase/ BeeBase The secret life of bees JBrowse 2013
http://hymenopteragenome.org/ant_genomes/ Ant Genomes Portal Ants GBrowse 2013
http://hymenopteragenome.org/nasonia/ NasoniaBase Nasonia wasp GBrowse 2013
http://icemangenome.net/ Ice Man Genome The genome of Ötzi the Iceman JBrowse 2013
http://ich.ciliate.org/ IchDB Ichthyophthirius multifiliis genome 2013
http://informatics.jax.org/ MGI 2013
http://inra.fr/lepidodb Lepido dB Lepidoptera database; covers Helicoverpa armigera and Spodoptera frugiperda GBrowse, CMap, Apollo, Chado 2012
http://www.inra.fr/meloidogyne_incognita Meloidogyne incognita Covers phytoparasitic root-knot nematode Meloidogyne incognita. Chado, GBrowse, Apollo 2013
http://insectacentral.org InsectaCentral Repository of insect transcriptomes Chado 2013
http://insects.eugenes.org/DroSpeGe/ DroSpeGe 200x
http://irfgc.irri.org/cgi-bin/gbrowse OryzaSNP 200x
http://iubio.bio.indiana.edu/ IUBio Archive Software and data from Indiana University; includes numerous resources, such as euGenes, DroSpeGe, wFleaBase, etc. Argos 2013
http://www.jcvi.org TIGR The Institute for Genomic Research Yes 200x
http://knowpulse2.usask.ca/portal/ KnowPulse: Pulse Crop Genomics & Breeding Chickpea, lentil, common bean, pea Tripal 2013
http://krithgenomics.drupalgardens.com/ K-RITH-Hopkins Genomics Web Portal JBrowse 2013
http://lgd.abcc.ncifcrf.gov/cgi-bin/gbrowse/cat/ GARFIELD Genome Annotation Resource Field Felis catus GBrowse 2013
http://www.livestockgenomics.csiro.au/ Livestock Genomics CSIRO Livestock Industries (LI) livestock genomics; covers bovines and ovines 2013
http://magi.plantgenomics.iastate.edu/ MAGI Maize Assembled Genomic Island 200x
http://maizegdb.org MaizeGDB Maize Genetics and Genomics DB 2013
http://www.marinegenomics.org Marine Genomics Multispecies marine organism database Tripal 2013
http://me.lzu.edu.cn/yak/ Yak Genome Database Yak genome 2013
http://www.medicinalgenomics.com/the-jane-ome/ The Jane-Ome Cannabis Genome Project, Medicinal Marijuana JBrowse 2013
http://mg.dna.affrc.go.jp/ MgEST DB Magnaporthe grisea ESTs GBrowse 2013
http://microb215.med.upenn.edu/gb2/gbrowse/phage_metagenomics/ Phage metagenomics GBrowse 2013
http://microsporidiadb.org MicrosporidiaDB Microsporidia (part of EupathDB) 2013
http://mips.helmholtz-muenchen.de/plant/triticeae/index.jsp MIPS Triticeae genomes database Barley, wheat, rye 2013
http://nabic.rda.go.kr/ NABIC RDA Various plant and animal genomes GBrowse_syn, GBrowse 2013
http://nypg.bio.nyu.edu/vicogenta/ Vicogenta Viewer for Comparing Genomes to Arabidopsis 200x
http://oikoarrays.biology.uiowa.edu/Oiko/ OikoBase genome expression database of Oikopleura dioica GBrowse 2013
http://www.omap.org/ OMAP Oryza Map Alignment Project 200x
http://www.opossumbase.org/ OpossumBase Monodelphis domestica Genomic Resources Database GBrowse, JBrowse 2013
http://orygenesdb.cirad.fr/ OryGenesDB 200x
http://paramecium.cgm.cnrs-gif.fr/ ParameciumDB Yes 200x
http://patricbrc.org PATRIC Pathosystems Resource Integration Center JBrowse 2013
http://phytozome.net/ Phytozome Numerous green plants GBrowse, BioMart 2013
http://piroplasmadb.org PiroplasmaDB Piroplasma (part of EupathDB) 2013
http://plasmodb.org PlasmoDB Plasmodium (part of EupathDB) 2013
http://popgenie.org/ PopGenIE The Populus Genome Integrative Explorer 200x
http://www.possumbase.org.nz/ PossumBase EST DB for the brushtail possum, Trichosurus vulpecula GBrowse 2013
http://pseudomonas.com/ PseudoCAP Pseudomonas Genome Database 200x
http://puma.princeton.edu/ PUMAdb Princeton Microarray Database, Chado 200x
http://qtaro.abr.affrc.go.jp/ QTARO QTL Annotation Rice Online GBrowse 2013
http://rapdb.dna.affrc.go.jp/ Rice Annotation Project DB GBrowse 2013
http://research.nhgri.nih.gov/mnemiopsis/ Mnemiopsis Genome Project The ctenophore Mnemiopsis leidyi JBrowse 2013
http://rgd.mcw.edu RGD Rat Genome Database 200x
http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice MSU Rice Genome Browser 2013
http://rnaspace.org/ RNAspace an integrated environment for non-coding RNA annotation JBrowse 2013
http://www.rosaceae.org Genome Database for Rosaceae Rosaceae species Tripal 2013
http://rulai.cshl.edu/cshlmpd/credit.html CSHLmpd Mammalian Promoter Database 2013
http://sgdlite.princeton.edu/ SGD Lite 200x
http://www.shigen.nig.ac.jp/barley/ BarleyDB Barley! GBrowse, CMap 2013
http://smedgd.neuro.utah.edu/ SmedGD Planaria ESTs Yes 2013
http://solgenomics.net/ Sol Genomics Network Yes 2013
http://soybase.org/ SoyBase USDA Soybean Genetics and Genomics Database No 200x
http://soybeangenome.siu.edu/ Soybean Gbrowse Database GBrowse 2013
http://spbase.org SpBase Genome sequence and annotations produced by the Baylor College of Medicine Human Genome Sequencing Center and the sea urchin research community. GBrowse, BioMart, Textpresso 2013
http://www.spirodelagenome.org/ Spirodela Genome GBrowse 2013
http://t1dbase.org/ T1DBase DB focussed on type 1 diabetes 2013
http://www.tigr.org/tigr-scripts/medicago/gbrowse_bacs.pl TIGR Medicago BACs 200x
http://toxodb.org ToxoDB Toxoplasma (part of EupathDB) 2013
http://treetfdb.bmep.riken.jp/index.pl 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) 2013
http://trichdb.org TrichDB Trichomonas (part of EupathDB) 2013
http://tritrypdb.org TriTrypDB Kinetoplastids (part of EupathDB) 2013
http://tropgenedb.cirad.fr/ TropGENE DB genetic and genomic information about tropical crops studied by Cirad. 200x
http://www.vaccinium.org/ Genomic DB for Vaccinium Blueberry, cranberry, lingonberry, other Vaccinium spp. Tripal 2013
http://vectorbase.org VectorBase Chado, DAS, Apollo Yes 2013
http://wfleabase.org/ wFleaBase Daphnia Yes 200x
http://wheat-urgi.versailles.inra.fr/Tools/Triannot-Pipeline/ TriAnnot Pipeline TriAnnot pipeline for automated plant genome annotation GBrowse 2013
http://wheat.pw.usda.gov/ GrainGenes GBrowse, CMap 2013
http://www.wheatgenome.info/ Wheat Genome Wheat 2013
http://www.wormbase.org WormBase 2013
http://www.xenbase.org/ Xenbase Xenopus 2013
http://xmap.ftdna.com/ Xmap Human X chromosome map for SNP and STR markers used in genetic genealogy and anthropology No 2013
http://yandell-lab.org/software/cgl/ CGL Comparative Genomics Library 2013
http://yeastgenome.org/ SGD S. cerevisiae resources 2013
http://ymap.ftdna.com/ Ymap Human Y chromosome map for SNP and STR markers used in genetic genealogy and anthropology No 2013
http://zfin.org/ ZFIN Zebrafish, Danio rerio GBrowse 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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