GMOD Users

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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 Agripestbase Agricultural pests 2013 Hessian fly part of Agripestbase 2013 Manduca sexta part of Agripestbase 2013 Amborella Genome Database Amborella GBrowse, Tripal 2014 AmoebaDB Amoeba (part of EupathDB) 2013 National Animal Genome Research Program Animal genomes! GBrowse 2013 ANISEED Ascidian Network for In Situ Expression and Embryological Data GBrowse 2013 Istituto di Genomica Applicata, Italy Plant resources GBrowse 2013 AphidBase Pea aphid genome Apollo, Chado, Galaxy, GBrowse, Cycs 2013 TAIR 2013 The Comprehensive Antibiotic Resistance Database Bioinformatics database of resistance genes, their products and associated phenotypes. Chado, GBrowse, Textpresso 2013 AspGD Aspergillus JBrowse, Sybil 2013 Arabidopsis Small RNA Project (ASRP) Arabidopsis JBrowse 2013 ATIDB Arabidopsis thaliana Integrated Database GBrowse 2013 Augustus AUGUSTUS predictions for Chlamydomonas GBrowse 2013 Avian Genomes Bird spp JBrowse 2013 Banana Genome Hub Bananas! Tripal 2013 Computational and Evolutionary Biology group Chlamydomonas FAIREseq experiments [1] GBrowse 2013 BeetleBase Tribolium castaneum Gbrowse, JBrowse, Chado 2013 Salmonella transcriptional map of S. Typhimurium JBrowse 2013 JHI Plant Bioinformatics Group James Hutton Institute Chado 2013 Barley SNP db Barley SNPs (at JHI) CMap 2013 ProFITS Protein Families Involved in the Transduction of Signalling (Maize) JBrowse, GBrowse 2013 Rubber Genome Browser (not accessible to public - Mar 2013) 2013 NGSmethDB NGSmethDB: A database for next-generation sequencing single-cytosine-resolution DNA methylation data JBrowse 2013 Pathway Tools Home of Pathway Tools 2013 SFGD Soybean Functional Genomics Database GBrowse 2013 BGD Bovine Genome Database Apollo, GBrowse 2013 Brachypodium JBrowse 2013 BrassicaDB Brassica species GBrowse 2014 BµG@Sbase Bacterial Microarray Group at St George's (BµG@S), London GBrowse 2013 ButterflyBase (part of InsectaCentral) Butterflies and moths GBrowse 2013 Cassavabase Cassava GBrowse, Pathway Tools 2014 Cacao Genome Database Cacao Tripal 2013 CGD Candida Genome Database 2013 Raetsch Lab @ MSKCC Machine learning approaches to genomics and medicine Galaxy, GBrowse 2013 Chlamydomonas Genome Browser and Wiki Chlamydomonas 2013 Chromosome 7 Annotation Project 2013 TGD Tetrahymena Genome Database 2013 Citrus sinensis annotation project Citrus sinensis GBrowse 2013 Citrus Genome Database Citrus Tripal 2013 Citrus Greening pathogens causing citrus greening (Huanglongbing or HLB), esp. Liberibacter 2013 CocoaGenDB Cocoa GBrowse, CMap 2013 Eimeria transcript database Annotated transcripts of protozoan parasites of the genus Eimeria 2013 TGI The Gene Index Project: uses ESTs and gene sequences to predict genes and variants GBrowse 2013 LIS Legume Information System CMap 2013 CoryneBase Corynebacterium, a small, rod-shaped, Gram-positive bacteria [2] JBrowse 2014 COSMIC Cancer Genome Project GBrowse 2014 The Bryophyte Genomics Resource - Physcomitrella patens Annotation GBrowse 2013 Cottongen Tripal 2013 Bioinformatics center of Institute of Microbial Technology (IMTECH), Chandigarh. Rhodococcus imtechensis sp. RKJ300 JBrowse 2013 CryptoDB Cryptosporidium (part of EupathDB) GBrowse, Cyc 2013 DOOR: a Database of prOkaryotic OpeRons Prokaryotic operons JBrowse 2013 ThioBase A database of thiopeptides featured in genetics and chemistry GBrowse_syn 2013 Database of Genomic Variants GBrowse 2013 Data-Intensive Academic Grid Provides a VM/cloud image of bioinf. software JBrowse, BioMart, Ergatis, etc. 2013 DictyBase Chado, GBrowse, more 2013 EcoBrowser E. coli transcriptome JBrowse 2013 EcoCyc 2013 EcoliWiki E. coli 2013 UKY Genome Projects University of Kentucky; numerous spp GBrowse 2013 eQTL browser eQTLs identified in recent studies in multiple tissues @ Pritchard lab, UChicago 2013 Equine Genome Equus caballus GBrowse 2013 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 Fagaceae Genomics Web Fagaceae spp, including oak, beech, chestnut, etc. Tripal 2013 FlyBase A Database of Drosophila Genes & Genomes Chado, GBrowse, more 2013 Flynet CisTrack (Cis-regulatory Module Tracking) extension for Drosophila JBrowse 2013 Fungal Genomes Fungal Genomics Resources 2013 FungiDB Fungal Genomics Resources 2013 A. fumigatus TIGR/Sanger Assembly 2013 S. nodorum Fungal Telomere Browser 2013 Fusarium virguliforme Genome Browser Soybean pathogen F. virguliforme GBrowse 2014 Cool Season Food Legume Database Cool season legumes, e.g. pea, lentil, chickpea, fava beans, etc. Tripal 2013 Evidence Project Psychiatric Genetics Human GBrowse 2013 JCVI J. Craig Venter Institute; offers numerous species 2013 JCVI Medicago @ J. Craig Venter Institute JBrowse, GBrowse, InterMine, Textpresso 2014 G-DOC Systems medicine platform for personalized oncology JBrowse 2013 GeneDB Pathogen Sequencing Unit Chado, JBrowse 2013 Generation Challenge Programme 2013 EcoLab @ INP Toulouse Medicago GBrowse, CMap 2013 Asian Genome Browser Human GBrowse 2013 Uni Oklahoma Advanced Center for Genome Technology Various spp GBrowse, JBrowse 2013 Uni of Oklahoma tomato group Solanaceae lycopersicum sequence JBrowse 2013 Southeast Fungal Biology Group Coprinus, Phanerochaete genome GBrowse 2013 Bovine QTL Viewer Bos taurus 2013 Genomes Unzipped Human -- personal genomic data made public JBrowse 2013 Istituto Agrario S. Michele all'Adige bioinformatics resources Apple, grape GBrowse, CMap 2013 Malaysian Oil Palm Genome Program (MyOPGP) Oil palm, Elaeis guineensis and E. oleifera MAKER 2014 Genoscope Multiple organisms GBrowse 2013 E. coli GenExpDB E. coli Gene Expression Database JBrowse 2013 Ghost Database Ciona intestinalis genomic and cDNA resources GBrowse 2013 GiardiaDB Giardia (part of EupathDB) 2013 CaPSID Computational Pathogen Sequence IDentification - open source platform for pathogen sequence identification JBrowse 2013 JBPC Generic Model Organism Database servers Huge set of GMOD/GBrowse resources covering many different species 2013 GNPannot Community system of structural and functional annotation supported by comparative genomics
Produces Chado controller
Chado, others 2013 Gramene Grain resources 2013 AfRicA DB African Rice Annotation DataBase GBrowse 2013 GResource Rice GBrowse 2014 HapMap 2013 Hardwood Genomics Project Hardwood tree spp Tripal 2013 Human Genome Diversity Project HGDP @ Pritchard lab, UChicago GBrowse 2013 Neem Genome Database Genome information, gene predictions, EST content and annotated proteins of Azadirachta indica plant species GBrowse 2013 HuRef Genome Project Human Ref Genome Project JBrowse 2013 BeeBase The secret life of bees JBrowse 2013 Ant Genomes Portal Ants GBrowse 2013 NasoniaBase Nasonia wasp GBrowse 2013 Ice Man Genome The genome of Ötzi the Iceman JBrowse 2013 IchDB Ichthyophthirius multifiliis genome 2013 ICRISAT India CMap 2013 Cucurbit Genomics Database Cucumbers, melons, squashes GBrowse, CMap 2013 Genome Biology Group @ Weatherall Institute of Molecular Medicine example GBrowse 2014 Mouse Genome Informatics Mus musculus 2013 Lepido dB Lepidoptera database; covers Helicoverpa armigera and Spodoptera frugiperda GBrowse, CMap, Apollo, Chado 2012 Meloidogyne incognita Covers phytoparasitic root-knot nematode Meloidogyne incognita. Chado, GBrowse, Apollo 2013 InsectaCentral Repository of insect transcriptomes Chado 2013 DroSpeGe 2013 iPlant Collaborative cyberinfrastructure and computational tools for plant science 2013 IUBio Archive Software and data from Indiana University; includes numerous resources, such as euGenes, DroSpeGe, wFleaBase, etc. Argos 2013 JCVI J. Craig Venter Institute Numerous GBrowse instances, Chado 2013 KBase Department of Energy Systems Biology Knowledgebase - community resource for predictive biology JBrowse (see KBase labs) 2013 KnowPulse: Pulse Crop Genomics & Breeding Chickpea, lentil, common bean, pea Tripal 2013 K-RITH-Hopkins Genomics Web Portal JBrowse 2013 GARFIELD Genome Annotation Resource Field Felis catus GBrowse 2013 Livestock Genomics CSIRO Livestock Industries (LI) livestock genomics; covers bovines and ovines 2013 LizardBase Anole (lizard) resources JBrowse, Galaxy 2013 MabsBase Mycobacterium abscessus database JBrowse 2013 MaizeGDB Maize Genetics and Genomics DB 2013 MarineGenomicsDB @ OIST, Japan Acropora digitifera, Pinctada fucata, Symbiodinium sp. clade B1, Ciona GBrowse 2013 Marine Genomics Multispecies marine organism database Tripal 2013 Yak Genome Database Yak genome GBrowse, GBrowse_syn 2013 The Jane-Ome Cannabis Genome Project, Medicinal Marijuana JBrowse 2013 MEGANTE Web-based annotation system [3] GBrowse 2013 MgEST DB Magnaporthe grisea ESTs GBrowse 2013 Phage metagenomics GBrowse 2013 MicrosporidiaDB Microsporidia (part of EupathDB) 2013 MIPS Triticeae genomes database Barley, wheat, rye 2013 MODEncode @ OICR Fly, worm GBrowse 2013 Rdecusdb Grooved Carpet shell clam Ruditapes decussatus [4] Tripal 2013 NABIC RDA Various plant and animal genomes GBrowse_syn, GBrowse 2013 Ascobase @ OSU Neurospora crassa GBrowse 2013 Nodai Genome Research Centre Mishimi ushi (aka Bos taurus) Japanese quail, rice GBrowse 2013 ViCoGentA Viewer for Comparing Genomes to Arabidopsis 2013 OikoBase genome expression database of Oikopleura dioica GBrowse 2013 OpossumBase Monodelphis domestica Genomic Resources Database GBrowse, JBrowse 2013 OryGenesDB Oryza sativa database GBrowse 2013 OryzaSNP Consortium Rice SNPs GBrowse 2013 ParameciumDB Chado, GBrowse, BioMart 2013 Nielsen Group Pathway Web Server Saccharopolyspora erythraea, plant data GBrowse, Pathway Tools 2013 PATRIC Pathosystems Resource Integration Center JBrowse 2013 PeanutBase Peanuts (not the cartoon) Tripal 2014 Phytozome Numerous green plants GBrowse, BioMart 2013 PiroplasmaDB Piroplasma (part of EupathDB) 2013 PlasmoDB Plasmodium (part of EupathDB) 2013 Plant Small RNA Genes WebServer small RNA-producing genes from plants JBrowse 2013 PIPA, next-gen sequencing analytics Tool for the analysis of RNA-seq transcriptomics data JBrowse 2013 PortEco Portal for E. coli data GBrowse, JBrowse, Pathway Tools 2013 PopGenIE The Populus Genome Integrative Explorer Galaxy 2013 PossumBase EST DB for the brushtail possum, Trichosurus vulpecula GBrowse 2013 SpudDB Potatoes! GBrowse, Chado 2013 Malay Human Genome Project Human GBrowse 2013 Youngstown State University Proteomics/Genomics Research Group Brachypodium GBrowse 2013 PseudoCAP Pseudomonas Genome Database GBrowse, Cyc 2013 QTARO QTL Annotation Rice Online GBrowse 2013 Rice Annotation Project DB GBrowse 2013 Mnemiopsis Genome Project The ctenophore Mnemiopsis leidyi JBrowse 2013 RGD Rat Genome Database 2013 MSU Rice Genome Browser 2013 RIKEN Multiple organisms GBrowse 2013 RNAbrowse integrated environment for analysis of RNA-seq results JBrowse, Galaxy, BioMart 2014 RNAspace an integrated environment for non-coding RNA annotation JBrowse 2013 Genome Database for Rosaceae Rosaceae species Tripal 2013 CSHLmpd Mammalian Promoter Database 2013 SANBI T. brucei 2013 TriticeaeGenome Barley at MIPS GBrowse 2014 Peach Genome Peaches @ Istituto di Genomica Applicata GBrowse 2013 YFGLite / SGD Lite Yeast Functional Genomics Database GBrowse 2013 BarleyDB Barley! GBrowse, CMap 2013 SkateBase Skate GBrowse 2013 SmedGD Planaria ESTs Chado 2013 Sol Genomics Network Chado 2013 SoyBase USDA Soybean Genetics and Genomics Database GBrowse, Cyc 2013 Soybean Gbrowse Database GBrowse 2013 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 Spotted Wing FlyBase Drosophila suzukii GBrowse, MAKER (use for annotation) 2013 Spirodela Genome the aquatic plant Spirodela GBrowse 2013 T1DBase DB focussed on type 1 diabetes 2013 TBrowse Integrative genomics map of Mycobacterium tuberculosis Chado, GBrowse 2013 Tomato Epigenome Database Tomato epigenome (surprise!) GBrowse 2014 Togo Genome genome database collection provided by the DBCLS JBrowse 2014 Tomato Genome 150 Tomato Genome ReSequencing project JBrowse 2013 ToxoDB Toxoplasma (part of EupathDB) 2013 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 TrichDB Trichomonas (part of EupathDB) 2013 Triticeae full-length CDS database [5] Brachypodium GBrowse 2013 TriTrypDB Kinetoplastids (part of EupathDB) 2013 TropGENE DB genetic and genomic information about tropical crops studied by Cirad. CMap 2013 Wheat @ URGI/INRA Wheat chr 1 GBrowse 2013 Genomic DB for Vaccinium Blueberry, cranberry, lingonberry, other Vaccinium spp. Tripal 2013 VectorBase Invertebrate vectors of human pathogens Chado, DAS, Apollo 2013 wFleaBase Daphnia Water Flea Genome Database Chado, BioMart, GBrowse 2013 TriAnnot Pipeline TriAnnot pipeline for automated plant genome annotation GBrowse 2013 GrainGenes GBrowse, CMap 2013 Wheat Genome Wheat 2013 Wild Soy DB Wild (and cultivated) soy bean genomes GBrowse, JBrowse 2013 WormBase C. elegans 2013 Xenbase Xenopus 2013 Xmap Human X chromosome map for SNP and STR markers used in genetic genealogy and anthropology GBrowse 2013 Drosophila yakuba JBrowse 2013 CGL Comparative Genomics Library 2013 SGD S. cerevisiae resources 2013 Ymap Human Y chromosome map for SNP and STR markers used in genetic genealogy and anthropology Gbrowse 2013 ZFIN Zebrafish, Danio rerio GBrowse 2013 RetrogeneDb [6] retrocopies JBrowse 2014 NGS Pipelines SeaBass brain and liver transcriptome BioMart; JBrowse 2014 Sigenae various agricultural spp BioMart, Galaxy 2014 Wageningen Bioinformatics Webportal Brassica rapa and similar JBrowse, MAKER 2014 Genome-wide Mycobacterium tuberculosis variation (GMTV) database [7] Mycobacterium tuberculosis JBrowse 2014 Camelina sativa oilseed GBrowse 2014 seeQTL searchable database for human eQTLs GBrowse 2014
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