The following is a selection of the websites (including organism databases, research groups, and software) using GBrowse, JBrowse, Chado, or some other popular component of GMOD. For a list of related publications see Publications.
Check out the map of GMOD users around the world!
| URL | Name | Description | Components | 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://amborella.org | Amborella Genome Database | Amborella | GBrowse, Tripal | 2014 |
| http://amoebadb.org | AmoebaDB | Amoeba (part of EupathDB) | 2013 | |
| http://animalgenome.org | National Animal Genome Research Program | Animal genomes! | GBrowse | 2013 |
| http://aniseed-ibdm.univ-mrs.fr/ | ANISEED | Ascidian Network for In Situ Expression and Embryological Data | GBrowse | 2013 |
| http://www.appliedgenomics.org/ | Istituto di Genomica Applicata, Italy | Plant resources | 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. | Chado, GBrowse, Textpresso | 2013 |
| http://aspergillusgenome.org/ | AspGD | Aspergillus | JBrowse, Sybil | 2013 |
| http://asrp.danforthcenter.org/ | Arabidopsis Small RNA Project (ASRP) | Arabidopsis | JBrowse | 2013 |
| http://atidb.org | ATIDB | Arabidopsis thaliana Integrated Database | GBrowse | 2013 |
| http://augustus.gobics.de/predictions/chlamydomonas/ | Augustus | AUGUSTUS predictions for Chlamydomonas | GBrowse | 2013 |
| http://aviangenomes.org | Avian Genomes | Bird spp | JBrowse | 2013 |
| http://banana-genome.cirad.fr/ | Banana Genome Hub | Bananas! | Tripal | 2013 |
| http://bce.uniandes.edu.co/ | Computational and Evolutionary Biology group | Chlamydomonas FAIREseq experiments [1] | GBrowse | 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/ | JHI Plant Bioinformatics Group | James Hutton Institute | Chado | 2013 |
| http://bioinf.scri.ac.uk/barley_snpdb/index.html | Barley SNP db | Barley SNPs (at JHI) | CMap | 2013 |
| 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://bioinfo2.ugr.es/NGSmethDB/ | NGSmethDB | NGSmethDB: A database for next-generation sequencing single-cytosine-resolution DNA methylation data | JBrowse | 2013 |
| http://bioinformatics.ai.sri.com/ptools/ | Pathway Tools | Home of Pathway Tools | 2013 | |
| http://bioinformatics.cau.edu.cn/SFGD/ | SFGD | Soybean Functional Genomics Database | GBrowse | 2013 |
| http://bovinegenome.org/ | BGD | Bovine Genome Database | Apollo, GBrowse | 2013 |
| http://www.brachybase.org/ | Brachypodium | JBrowse | 2013 | |
| http://brassicadb.org/brad/ | BrassicaDB | Brassica species | GBrowse | 2014 |
| http://bugs.sgul.ac.uk/bugsbase/ | BµG@Sbase | Bacterial Microarray Group at St George's (BµG@S), London | GBrowse | 2013 |
| http://butterflybase.ice.mpg.de/ | ButterflyBase (part of InsectaCentral) | Butterflies and moths | GBrowse | 2013 |
| http://www.cassavabase.org/ | Cassavabase | Cassava | GBrowse, Pathway Tools | 2014 |
| http://www.cacaogenomedb.org | Cacao Genome Database | Cacao | Tripal | 2013 |
| http://www.candidagenome.org/cgi-bin/gbrowse/candida_20/ | CGD | Candida Genome Database | 2013 | |
| http://cbio.mskcc.org/raetschlab/ | Raetsch Lab @ MSKCC | Machine learning approaches to genomics and medicine | Galaxy, GBrowse | 2013 |
| http://chlamy.info/ | Chlamydomonas Genome Browser and Wiki | Chlamydomonas | 2013 | |
| http://www.chr7.org/cgi-bin/gbrowse/gbrowse/chr7_v2/ | Chromosome 7 Annotation Project | 2013 | ||
| http://www.ciliate.org/ | TGD | Tetrahymena Genome Database | 2013 | |
| http://citrus.hzau.edu.cn/orange/ | Citrus sinensis annotation project | Citrus sinensis | GBrowse | 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://cocoagendb.cirad.fr/ | CocoaGenDB | Cocoa | GBrowse, CMap | 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://corynebacterium.um.edu.my/index.php/home/main | CoryneBase | Corynebacterium, a small, rod-shaped, Gram-positive bacteria [2] | JBrowse | 2014 |
| http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/ | COSMIC | Cancer Genome Project | GBrowse | 2014 |
| http://www.cosmoss.org | cosmoss.org | The Bryophyte Genomics Resource - Physcomitrella patens Annotation | GBrowse | 2013 |
| http://www.cottongen.org/ | Cottongen | Tripal | 2013 | |
| http://crdd.osdd.net/jbrowse/index.html?data=/raghava/genomesrs/rhodo-imt/data | Bioinformatics center of Institute of Microbial Technology (IMTECH), Chandigarh. | Rhodococcus imtechensis sp. RKJ300 | JBrowse | 2013 |
| http://cryptodb.org | CryptoDB | Cryptosporidium (part of EupathDB) | GBrowse, Cyc | 2013 |
| http://csbl.bmb.uga.edu/DOOR/ | DOOR: a Database of prOkaryotic OpeRons | Prokaryotic operons | JBrowse | 2013 |
| http://db-mml.sjtu.edu.cn/ThioFinder/search.html | ThioBase | A database of thiopeptides featured in genetics and chemistry | GBrowse_syn | 2013 |
| http://dgv.tcag.ca/ | Database of Genomic Variants | GBrowse | 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 | Chado, GBrowse, more | 2013 | |
| http://ecobrowser.biosino.org | EcoBrowser | E. coli transcriptome | JBrowse | 2013 |
| http://ecocyc.org/ | EcoCyc | 2013 | ||
| http://ecoliwiki.net | EcoliWiki | E. coli | 2013 | |
| http://www.endophyte.uky.edu/ | UKY Genome Projects | University of Kentucky; numerous spp | GBrowse | 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 | GBrowse | 2013 |
| 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 | Chado, GBrowse, more | 2013 |
| https://www.cistrack.org/flynet/site/ | Flynet | CisTrack (Cis-regulatory Module Tracking) extension for Drosophila | JBrowse | 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://fvgbrowse.agron.iastate.edu/ | Fusarium virguliforme Genome Browser | Soybean pathogen F. virguliforme | GBrowse | 2014 |
| http://gabcsfl.org | Cool Season Food Legume Database | Cool season legumes, e.g. pea, lentil, chickpea, fava beans, etc. | Tripal | 2013 |
| http://gbrowse.csbio.unc.edu/cgi-bin/gb2/gbrowse/slep/ | Evidence Project Psychiatric Genetics | Human | GBrowse | 2013 |
| http://gbrowse.jcvi.org/gbrowse/ | JCVI | J. Craig Venter Institute; offers numerous species | 2013 | |
| http://jcvi.org/medicago/ | JCVI | Medicago @ J. Craig Venter Institute | JBrowse, GBrowse, InterMine, Textpresso | 2014 |
| 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 | 2013 | ||
| http://genolab.inp-toulouse.fr/gb2/gbrowse/medic3/ | EcoLab @ INP Toulouse | Medicago | GBrowse, CMap | 2013 |
| http://genome.igib.res.in/cgi-bin/gbrowse/AsianGenome/ | Asian Genome Browser | Human | GBrowse | 2013 |
| http://www.genome.ou.edu/ | Uni Oklahoma Advanced Center for Genome Technology | Various spp | GBrowse, JBrowse | 2013 |
| http://www.genome.ou.edu/tomato.html | Uni of Oklahoma tomato group | Solanaceae lycopersicum sequence | JBrowse | 2013 |
| http://genome.semo.edu/ | Southeast Fungal Biology Group | Coprinus, Phanerochaete genome | GBrowse | 2013 |
| http://genomes.sapac.edu.au/bovineqtl/ | Bovine QTL Viewer | Bos taurus | 2013 | |
| http://www.genomesunzipped.org/jbrowse/ | Genomes Unzipped | Human -- personal genomic data made public | JBrowse | 2013 |
| http://genomics.research.iasma.it/ | Istituto Agrario S. Michele all'Adige bioinformatics resources | Apple, grape | GBrowse, CMap | 2013 |
| http://genomsawit.mpob.gov.my/genomsawit/ | Malaysian Oil Palm Genome Program (MyOPGP) | Oil palm, Elaeis guineensis and E. oleifera | MAKER | 2014 |
| 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://ghost.zool.kyoto-u.ac.jp/cgi-bin/gb2/gbrowse/kh/ | Ghost Database | Ciona intestinalis genomic and cDNA resources | GBrowse | 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.gnpannot.org/ | GNPannot | Community system of structural and functional annotation supported
by comparative genomics Produces Chado controller |
Chado, others | 2013 |
| http://www.gramene.org | Gramene | Grain resources | 2013 | |
| http://green.dna.affrc.go.jp/Og/ | AfRicA DB | African Rice Annotation DataBase | GBrowse | 2013 |
| http://gresource.hzau.edu.cn/resource/resource.html | GResource | Rice | GBrowse | 2014 |
| 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 | GBrowse | 2013 |
| http://www.hpppi.iicb.res.in/neemgdb/ | Neem Genome Database | Genome information, gene predictions, EST content and annotated proteins of Azadirachta indica plant species | GBrowse | 2013 |
| http://huref.nimbusinformatics.com/ | HuRef Genome Project | Human Ref Genome Project | 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://ich.ciliate.org/ | IchDB | Ichthyophthirius multifiliis genome | 2013 | |
| http://cmap.icrisat.ac.in/cmap/index_public.html | ICRISAT India | CMap | 2013 | |
| http://www.icugi.org | Cucurbit Genomics Database | Cucumbers, melons, squashes | GBrowse, CMap | 2013 |
| http://www.imm.ox.ac.uk/mrc-molecular-haematology-unit | Genome Biology Group @ Weatherall Institute of Molecular Medicine | example | GBrowse | 2014 |
| http://informatics.jax.org/ | Mouse Genome Informatics | Mus musculus | 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 | 2013 | ||
| http://www.iplantcollaborative.org/ | iPlant Collaborative | cyberinfrastructure and computational tools for plant science | 2013 | |
| 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 | JCVI | J. Craig Venter Institute | Numerous GBrowse instances, Chado | 2013 |
| http://kbase.science.energy.gov/labs/ | KBase | Department of Energy Systems Biology Knowledgebase - community resource for predictive biology | JBrowse (see KBase labs) | 2013 |
| 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://lizardbase.org/pages/jbrowse.html | LizardBase | Anole (lizard) resources | JBrowse, Galaxy | 2013 |
| http://mabscessus.um.edu.my/ | MabsBase | Mycobacterium abscessus database | JBrowse | 2013 |
| http://maizegdb.org | MaizeGDB | Maize Genetics and Genomics DB | 2013 | |
| http://marinegenomics.oist.jp/genomes/gallery | MarineGenomicsDB @ OIST, Japan | Acropora digitifera, Pinctada fucata, Symbiodinium sp. clade B1, Ciona | GBrowse | 2013 |
| http://www.marinegenomics.org | Marine Genomics | Multispecies marine organism database | Tripal | 2013 |
| http://me.lzu.edu.cn/yak/ | Yak Genome Database | Yak genome | GBrowse, GBrowse_syn | 2013 |
| http://www.medicinalgenomics.com/the-jane-ome/ | The Jane-Ome | Cannabis Genome Project, Medicinal Marijuana | JBrowse | 2013 |
| https://megante.dna.affrc.go.jp/ | MEGANTE | Web-based annotation system [3] | GBrowse | 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://modencode.oicr.on.ca/fgb2/gbrowse/fly/ | MODEncode @ OICR | Fly, worm | GBrowse | 2013 |
| http://morse-ccmar.ualg.pt/edge/ | Rdecusdb | Grooved Carpet shell clam Ruditapes decussatus [4] | Tripal | 2013 |
| http://nabic.rda.go.kr/ | NABIC RDA | Various plant and animal genomes | GBrowse_syn, GBrowse | 2013 |
| http://ascobase.cgrb.oregonstate.edu/cgi-bin/gb2/gbrowse/ncrassa_public/ | Ascobase @ OSU | Neurospora crassa | GBrowse | 2013 |
| http://www.nodai-genome.org/?lang=en | Nodai Genome Research Centre | Mishimi ushi (aka Bos taurus) Japanese quail, rice | GBrowse | 2013 |
| http://nypg.bio.nyu.edu/vicogenta/ | ViCoGentA | Viewer for Comparing Genomes to Arabidopsis | 2013 | |
| http://oikoarrays.biology.uiowa.edu/Oiko/ | OikoBase | genome expression database of Oikopleura dioica | GBrowse | 2013 |
| http://www.opossumbase.org/ | OpossumBase | Monodelphis domestica Genomic Resources Database | GBrowse, JBrowse | 2013 |
| http://orygenesdb.cirad.fr/ | OryGenesDB | Oryza sativa database | GBrowse | 2013 |
| http://www.oryzasnp.org/ | OryzaSNP Consortium | Rice SNPs | GBrowse | 2013 |
| http://paramecium.cgm.cnrs-gif.fr/ | ParameciumDB | Chado, GBrowse, BioMart | 2013 | |
| http://pathway.aibn.uq.edu.au/ | Nielsen Group Pathway Web Server | Saccharopolyspora erythraea, plant data | GBrowse, Pathway Tools | 2013 |
| http://patricbrc.org | PATRIC | Pathosystems Resource Integration Center | JBrowse | 2013 |
| http://peanutbase.org/ | PeanutBase | Peanuts (not the cartoon) | Tripal | 2014 |
| http://www.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://plantsmallrnagenes.psu.edu/ | Plant Small RNA Genes WebServer | small RNA-producing genes from plants | JBrowse | 2013 |
| http://pipa.biolab.si/hp/index.html | PIPA, next-gen sequencing analytics | Tool for the analysis of RNA-seq transcriptomics data | JBrowse | 2013 |
| http://porteco.org | PortEco | Portal for E. coli data | GBrowse, JBrowse, Pathway Tools | 2013 |
| http://popgenie.org/ | PopGenIE | The Populus Genome Integrative Explorer | Galaxy | 2013 |
| http://www.possumbase.org.nz/ | PossumBase | EST DB for the brushtail possum, Trichosurus vulpecula | GBrowse | 2013 |
| http://potato.plantbiology.msu.edu/index.shtml | SpudDB | Potatoes! | GBrowse, Chado | 2013 |
| http://promisegenome.uitm.edu.my/cgi-bin/gbrowse/hgmalay/ | Malay Human Genome Project | Human | GBrowse | 2013 |
| http://proteomics.ysu.edu/tools/index.html | Youngstown State University Proteomics/Genomics Research Group | Brachypodium | GBrowse | 2013 |
| http://pseudomonas.com/ | PseudoCAP | Pseudomonas Genome Database | GBrowse, Cyc | 2013 |
| 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 | 2013 | |
| http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice | MSU Rice Genome Browser | 2013 | ||
| http://rpop.psc.riken.jp/cgi-bin/gbrowse/pop_ver20080425/ | RIKEN | Multiple organisms | GBrowse | 2013 |
| http://bioinfo.genotoul.fr/RNAbrowse | RNAbrowse | integrated environment for analysis of RNA-seq results | JBrowse, Galaxy, BioMart | 2014 |
| 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://www.sanbi.ac.za | SANBI | T. brucei | 2013 | |
| http://seacow.helmholtz-muenchen.de/cgi-bin/gb2/gbrowse/Barley_PhysMap/ | TriticeaeGenome | Barley at MIPS | GBrowse | 2014 |
| http://services.appliedgenomics.org/projects/drupomics/ | Peach Genome | Peaches @ Istituto di Genomica Applicata | GBrowse | 2013 |
| http://sgdlite.princeton.edu/ | YFGLite / SGD Lite | Yeast Functional Genomics Database | GBrowse | 2013 |
| http://www.shigen.nig.ac.jp/barley/ | BarleyDB | Barley! | GBrowse, CMap | 2013 |
| http://skatebase.org/ | SkateBase | Skate | GBrowse | 2013 |
| http://smedgd.neuro.utah.edu/ | SmedGD | Planaria ESTs | Chado | 2013 |
| http://solgenomics.net/ | Sol Genomics Network | Chado | 2013 | |
| http://soybase.org/ | SoyBase | USDA Soybean Genetics and Genomics Database | GBrowse, Cyc | 2013 |
| 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://spottedwingflybase.oregonstate.edu/ | Spotted Wing FlyBase | Drosophila suzukii | GBrowse, MAKER (use for annotation) | 2013 |
| http://spirodelagenome.org/ | Spirodela Genome | the aquatic plant Spirodela | GBrowse | 2013 |
| http://t1dbase.org/ | T1DBase | DB focussed on type 1 diabetes | 2013 | |
| http://tbrowse.osdd.net/ | TBrowse | Integrative genomics map of Mycobacterium tuberculosis | Chado, GBrowse | 2013 |
| http://ted.bti.cornell.edu/epigenome/index.html | Tomato Epigenome Database | Tomato epigenome (surprise!) | GBrowse | 2014 |
| http://togogenome.org/ | Togo Genome | genome database collection provided by the DBCLS | JBrowse | 2014 |
| http://www.tomatogenome.net/ | Tomato Genome | 150 Tomato Genome ReSequencing project | JBrowse | 2013 |
| 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://trifldb.psc.riken.jp/v3/index.pl | Triticeae full-length CDS database [5] | Brachypodium | GBrowse | 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. | CMap | 2013 |
| https://urgi.versailles.inra.fr/gb2/gbrowse/wheat_phys_pub/ | Wheat @ URGI/INRA | Wheat chr 1 | GBrowse | 2013 |
| http://www.vaccinium.org/ | Genomic DB for Vaccinium | Blueberry, cranberry, lingonberry, other Vaccinium spp. | Tripal | 2013 |
| http://vectorbase.org | VectorBase | Invertebrate vectors of human pathogens | Chado, DAS, Apollo | 2013 |
| http://wfleabase.org/ | wFleaBase | Daphnia Water Flea Genome Database | Chado, BioMart, GBrowse | 2013 |
| 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://wildsoydb.org/ | Wild Soy DB | Wild (and cultivated) soy bean genomes | GBrowse, JBrowse | 2013 |
| http://www.wormbase.org | WormBase | C. elegans | 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 | GBrowse | 2013 |
| http://yakuba.uchicago.edu/ | Drosophila yakuba | JBrowse | 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 | Gbrowse | 2013 |
| http://zfin.org/ | ZFIN | Zebrafish, Danio rerio | GBrowse | 2013 |
| http://retrogenedb.amu.edu.pl | RetrogeneDb [6] | retrocopies | JBrowse | 2014 |
| http://ngspipelines.toulouse.inra.fr:9019 | NGS Pipelines | SeaBass brain and liver transcriptome | BioMart; JBrowse | 2014 |
| http://sigenae.org | Sigenae | various agricultural spp | BioMart, Galaxy | 2014 |
| http://www.bioinformatics.nl/brassica/turnip | Wageningen Bioinformatics Webportal | Brassica rapa and similar | JBrowse, MAKER | 2014 |
| http://mtb.dobzhanskycenter.org | Genome-wide Mycobacterium tuberculosis variation (GMTV) database [7] | Mycobacterium tuberculosis | JBrowse | 2014 |
| http://www.camelinadb.ca/ | Camelina sativa | oilseed | GBrowse | 2014 |
| http://gbrowse.csbio.unc.edu/cgi-bin/gb2/gbrowse/seeqtl/ | seeQTL | searchable database for human eQTLs | GBrowse | 2014 |
<ref> tag; no text was provided for refs
named DOI:10.1371.2Fjournal.pone.0079909<ref> tag; no text was provided for refs
named DOI:10.1371.2Fjournal.pone.0086318<ref> tag; no text was provided for refs
named DOI:10.1093.2Fpcp.2Fpct157<ref> tag; no text was provided for refs
named DOI:10.1186.2F1471-2164-14-741<ref> tag; no text was provided for refs
named DOI:10.1371.2Fjournal.pone.0075265<ref> tag; no text was provided for refs
named doi:10.1093.2Fmolbev.2Fmsu139<ref> tag; no text was provided for refs
named doi:10.1186.2F1471-2164-15-308