Difference between revisions of "GMOD Users"

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==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]].
  
−
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.
+
<!-- At the bottom of the page there is a list of [[GBrowse]] users. -->
 +
Check out the [http://gmod.org/worldwide.html map of GMOD users around the world]!
  
  
−
{| border="1" cellspacing="0"
+
{| class="wikitable sortable"
 +
!URL
 
!Name
 
!Name
 
!Description
 
!Description
−
!Location
+
!Components
−
!Chado
+
!Checked
 
|-
 
|-
−
|A. fumigatus TIGR/Sanger Assembly
+
| http://agripestbase.org || Agripestbase || Agricultural pests || || 2013
−
|
+
−
|http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/A_fumigatus_tigr_tel_100k
+
−
|
+
 
|-
 
|-
−
|ANISEED
+
| http://agripestbase.org/hessianfly || Hessian fly || part of Agripestbase || || 2013
−
|Ascidian Network for In Situ Expression and Embryological Data
+
−
|http://crfb.univ-mrs.fr/ciona-bin/gbrowse/intestinalis/
+
−
|
+
 
|-
 
|-
−
|AntonosporaDB
+
| http://agripestbase.org/manduca || Manduca sexta || part of Agripestbase || || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/antonospora01
+
−
|
+
 
|-
 
|-
−
|ApiDB
+
| http://amborella.org || Amborella Genome Database || Amborella || GBrowse, Tripal || 2014
−
|
+
−
|http://apidb.org/apidb/
+
−
|
+
 
|-
 
|-
−
|ATIDB
+
| http://amoebadb.org || AmoebaDB || Amoeba (part of EupathDB) || || 2013
−
|Arabidopsis
+
−
|http://atidb.org
+
−
|
+
 
|-
 
|-
−
|Aureococcus
+
| http://animalgenome.org || National Animal Genome Research Program || Animal genomes! || GBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/aureococcus
+
−
|
+
 
|-
 
|-
−
|AZM-to-BAC Viewer
+
| http://aniseed-ibdm.univ-mrs.fr/ || ANISEED || Ascidian Network for In Situ Expression and Embryological Data || GBrowse || 2013
−
|
+
−
|http://maizeapache.ddpsc.org/cgi-bin/gbrowse.cgi?source=01_azm2bac
+
−
|
+
 
|-
 
|-
−
|AZM-to-Gene Viewer
+
| http://www.appliedgenomics.org/ || Istituto di Genomica Applicata, Italy || Plant resources || GBrowse || 2013
−
|
+
−
|http://maizeapache.ddpsc.org/cgi-bin/gbrowse.cgi?source=02_azm2gene
+
−
|
+
 
|-
 
|-
−
|BeeBase
+
| http://www.aphidbase.com/ || AphidBase || Pea aphid genome || Apollo, Chado, Galaxy, GBrowse, Cycs || 2013
−
|
+
−
|http://racerx00.tamu.edu/bee_resources.html
+
−
|
+
 
|-
 
|-
−
|BeetleBase
+
| http://www.arabidopsis.org || [[:Category:TAIR|TAIR]] ||  ||  || 2013
−
|Gbrowse UI
+
−
|http://www.bioinformatics.ksu.edu/BeetleBase/
+
−
|Yes
+
 
|-
 
|-
−
|BGD
+
| http://arpcard.mcmaster.ca/ || The Comprehensive Antibiotic Resistance Database || Bioinformatics database of resistance genes, their products and associated phenotypes. || Chado, GBrowse, Textpresso || 2013
−
|Bovine Genome Database
+
−
|http://bovinegenome.org/
+
−
|
+
 
|-
 
|-
−
|BioHealthBase
+
| http://aspergillusgenome.org/ || AspGD || Aspergillus || JBrowse, Sybil || 2013
−
|BioDefense Public Health Database
+
−
|http://www.biohealthbase.org/GSearch/
+
−
|
+
 
|-
 
|-
−
|Blochmannia pennsylvanicus
+
| http://asrp.danforthcenter.org/ || Arabidopsis Small RNA Project (ASRP) || Arabidopsis || JBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/blochmannia06
+
−
|
+
 
|-
 
|-
−
|Bovine QTL Viewer
+
| http://atidb.org || ATIDB || Arabidopsis thaliana Integrated Database || GBrowse || 2013
−
|
+
−
|http://bovineqtl.tamu.edu
+
−
|
+
 
|-
 
|-
−
|Brachionus plicatilis A
+
| http://augustus.gobics.de/predictions/chlamydomonas/ || Augustus || AUGUSTUS predictions for Chlamydomonas || GBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/bplicatilisa
+
−
|
+
 
|-
 
|-
−
|Brachionus plicatilis B
+
| http://aviangenomes.org || Avian Genomes || Bird spp || JBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/bplicatilisb
+
−
|
+
 
|-
 
|-
−
|Cattle EST Gene Family Database
+
| http://banana-genome.cirad.fr/ || Banana Genome Hub || Bananas! || Tripal || 2013
−
|
+
−
|http://racerx00.tamu.edu/cgi-test/searchCattleDatabase.html
+
−
|
+
 
|-
 
|-
−
|CGD
+
| http://bce.uniandes.edu.co/ || Computational and Evolutionary Biology group || Chlamydomonas FAIREseq experiments <ref name="DOI:10.1371/journal.pone.0079909" /> || GBrowse || 2013
−
|Candida Genome Database
+
−
|http://www.candidagenome.org/cgi-bin/gbrowse/candida_20/
+
−
|
+
 
|-
 
|-
−
|CGL
+
| http://beetlebase.org/ || BeetleBase || ''Tribolium castaneum'' || Gbrowse, JBrowse, Chado || 2013
−
|Comparative Genomics Library
+
−
|http://www.yandell-lab.org/cgl/
+
−
|
+
 
|-
 
|-
−
|ChromDB
+
| http://bioinf.gen.tcd.ie/jbrowse/SL1344/ || Salmonella || transcriptional map of S. Typhimurium || JBrowse || 2013
−
|Plant Chromatin Database
+
−
|http://www.chromdb.org/
+
−
|
+
 
|-
 
|-
−
|Chromosome 7 Annotation Project
+
| http://bioinf.hutton.ac.uk/public/ || JHI Plant Bioinformatics Group || James Hutton Institute || Chado || 2013
−
|
+
−
|http://www.chr7.org/cgi-bin/gbrowse/gbrowse/chr7_v2
+
−
|
+
 
|-
 
|-
−
|CryptoDB
+
| http://bioinf.scri.ac.uk/barley_snpdb/index.html || Barley SNP db || Barley SNPs (at JHI) || CMap || 2013
−
|
+
−
|http://cryptodb.org
+
−
|
+
 
|-
 
|-
−
|CSHLmpd
+
| http://bioinfo.cau.edu.cn/ProFITS/index.php || ProFITS || Protein Families Involved in the Transduction of Signalling (Maize) || JBrowse, GBrowse || 2013
−
|Mammalian Promoter Database
+
−
|http://rulai.cshl.edu/cshlmpd/credit.html
+
−
|
+
 
|-
 
|-
−
|Database of Genomic Variants
+
| http://bioinfo.ccbusm.edu.my/cgi-bin/gb2/gbrowse/Rubber/ || Rubber Genome Browser || (not accessible to public - Mar 2013) ||  || 2013
−
|
+
−
|http://projects.tcag.ca/variation/cgi-bin/gbrowse/hg17
+
−
|
+
 
|-
 
|-
−
|DictyBase
+
| http://bioinfo2.ugr.es/NGSmethDB/ || NGSmethDB || NGSmethDB: A database for next-generation sequencing single-cytosine-resolution DNA methylation data || JBrowse || 2013
−
|
+
−
|http://www.dictybase.org
+
−
|Yes
+
 
|-
 
|-
−
|DroSpeGe
+
| http://bioinformatics.ai.sri.com/ptools/ || [[Pathway Tools]] || || Home of Pathway Tools || 2013
−
|
+
−
|http://insects.eugenes.org/DroSpeGe/
+
−
|
+
 
|-
 
|-
−
|EcoCyc
+
| http://bioinformatics.cau.edu.cn/SFGD/ || SFGD || Soybean Functional Genomics  Database || GBrowse || 2013
−
|
+
−
|http://ecocyc.org/
+
−
|
+
 
|-
 
|-
−
|Emiliania huxleyi
+
| http://bovinegenome.org/ || BGD || Bovine Genome Database || Apollo, GBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/emiliania_huxleyi
+
−
|
+
 
|-
 
|-
−
|Enterocytozoon bieneusi
+
| http://www.brachybase.org/ || Brachypodium || || JBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/ebieneusi
+
−
|
+
 
|-
 
|-
−
|Environmental Sampling Site 396, Fosmid 68
+
| http://brassicadb.org/brad/ || BrassicaDB || Brassica species || GBrowse || 2014
−
|
+
−
|http://gmod.mbl.edu/perl/site/env396_fosmid68
+
−
|
+
 
|-
 
|-
−
|Environmental Sampling Site 396, Fosmid 87
+
| http://bugs.sgul.ac.uk/bugsbase/ || BµG@Sbase || Bacterial Microarray Group at St George's (BµG@S), London || GBrowse|| 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/env396_fosmid87
+
−
|
+
 
|-
 
|-
−
|Environmental Sampling Site 396, Fosmids_6_ 56
+
| http://butterflybase.ice.mpg.de/ || ButterflyBase (part of InsectaCentral) || Butterflies and moths || GBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/env396_fosmids_6_56
+
−
|
+
 
|-
 
|-
−
|Environmental Sampling Site Loihi, Red Clone 1
+
| http://www.cassavabase.org/ || Cassavabase || Cassava || GBrowse, Pathway Tools || 2014
−
|
+
−
|http://gmod.mbl.edu/perl/site/envloihi_clone1
+
−
|
+
 
|-
 
|-
−
|Environmental Sampling Site Loihi, Red Clone 2
+
| http://www.cacaogenomedb.org || Cacao Genome Database || Cacao || Tripal || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/envloihi_clone2
+
−
|
+
 
|-
 
|-
−
|FlyBase
+
| http://www.candidagenome.org/cgi-bin/gbrowse/candida_20/ || CGD || Candida Genome Database ||  || 2013
−
|
+
−
|http://www.flybase.org
+
−
|Yes
+
 
|-
 
|-
−
|Fungal Comparitive Genomics
+
| http://cbio.mskcc.org/raetschlab/ || Raetsch Lab @ MSKCC || Machine learning approaches to genomics and medicine || Galaxy, GBrowse || 2013
−
|
+
−
|http://fungal.genome.duke.edu/
+
−
|
+
 
|-
 
|-
−
|Fungal Telomere Browser
+
| http://chlamy.info/ || Chlamydomonas Genome Browser and Wiki || Chlamydomonas || || 2013
−
|
+
−
|http://genome.kbrin.uky.edu/fungi_tel/browser.html
+
−
|
+
 
|-
 
|-
−
|Gallus gallus
+
| http://www.chr7.org/cgi-bin/gbrowse/gbrowse/chr7_v2/ || Chromosome 7 Annotation Project ||  ||  || 2013
−
|Gallus gallus SAGE
+
<!-- ??
−
|http://gmod.mbl.edu/perl/site/g_gallus
+
−
|
+
 
|-
 
|-
−
|Gallus Genome Browser
+
| http://www.chromdb.org/ || ChromDB || Plant Chromatin Database ||  || 200x
−
|
+
-->
−
|http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chicken
+
−
|
+
 
|-
 
|-
−
|GeneDB
+
| http://www.ciliate.org/ || TGD || Tetrahymena Genome Database ||  || 2013
−
|Pathogen Sequenceing Unit
+
−
|http://www.genedb.org
+
−
|Yes
+
 
|-
 
|-
−
|giardia14
+
| http://citrus.hzau.edu.cn/orange/ || Citrus sinensis annotation project || ''Citrus sinensis'' || GBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/giardia14
+
−
|
+
 
|-
 
|-
−
|GiardiaDB
+
| http://www.citrusgenomedb.org || Citrus Genome Database || Citrus || Tripal || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/giardia?page=intro
+
−
|
+
 
|-
 
|-
−
|GrainGenes
+
| http://citrusgreening.org/ || Citrus Greening || pathogens causing citrus greening (Huanglongbing or HLB), esp. ''Liberibacter'' ||  || 2013
−
|
+
−
|http://wheat.pw.usda.gov/
+
−
|
+
 
|-
 
|-
−
|Gramene
+
| http://cocoagendb.cirad.fr/ || CocoaGenDB || Cocoa || GBrowse, CMap || 2013
−
|
+
−
|http://www.gramene.org
+
−
|
+
 
|-
 
|-
−
|HapMap
+
| http://www.coccidia.icb.usp.br/eimeriatdb/ || ''Eimeria'' transcript database || Annotated transcripts of protozoan parasites of the genus Eimeria ||  || 2013
−
|
+
−
|http://www.hapmap.org/cgi-perl/gbrowse/
+
−
|
+
 
|-
 
|-
−
|Human 2q33
+
| http://compbio.dfci.harvard.edu/tgi/ || TGI || The Gene Index Project: uses ESTs and gene sequences to predict genes and variants || GBrowse || 2013
−
|
+
−
|http://t1dbase.cimr.cam.ac.uk/cgi-bin/gbrowse/2q33/
+
−
|
+
 
|-
 
|-
−
|Human Genome Segmental Duplication Database
+
| http://www.comparative-legumes.org/ || LIS || Legume Information System || CMap || 2013
−
|
+
−
|http://projects.tcag.ca/cgi-bin/duplication/dupbrowse/human_b36
+
−
|
+
 
|-
 
|-
−
|IVDB
+
| http://corynebacterium.um.edu.my/index.php/home/main || CoryneBase || ''Corynebacterium'', a small, rod-shaped, Gram-positive bacteria <ref name="DOI:10.1371/journal.pone.0086318" /> || JBrowse || 2014
−
|Influenza Virus Database
+
−
|http://influenza.genomics.org.cn/
+
−
|
+
 
|-
 
|-
−
|Leishmania tarentolae RNA editing database
+
| http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/ || COSMIC || Cancer Genome Project || GBrowse || 2014
−
|
+
−
|http://gmod.mbl.edu/gb/gbrowse/ltgrna
+
−
|
+
 
|-
 
|-
−
|LIS
+
| http://www.cosmoss.org || cosmoss.org || The Bryophyte Genomics Resource - ''Physcomitrella patens'' Annotation || GBrowse || 2013
−
|Legume Information System
+
−
|http://www.comparative-legumes.org/
+
−
|
+
 
|-
 
|-
−
|MAGI
+
| http://www.cottongen.org/ || Cottongen ||  || Tripal || 2013
−
|Maize Assembled Genomic Island
+
−
|http://magi.plantgenomics.iastate.edu/
+
−
|
+
 
|-
 
|-
−
|Marinobacter aquaeolei
+
| 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://gmod.mbl.edu/perl/site/marinobacter_jgi
+
−
|
+
 
|-
 
|-
−
|Marinobacter aquaeolei FOSMID 38/33.
+
| http://cryptodb.org || CryptoDB || Cryptosporidium (part of EupathDB) || GBrowse, Cyc|| 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/marinobacter
+
−
|
+
 
|-
 
|-
−
|MGI
+
| http://csbl.bmb.uga.edu/DOOR/ || DOOR: a Database of prOkaryotic OpeRons || Prokaryotic operons || JBrowse || 2013
−
|
+
−
|http://www.informatics.jax.org/
+
−
|
+
 
|-
 
|-
−
|Non-Human Segmental Duplication Database
+
| http://db-mml.sjtu.edu.cn/ThioFinder/search.html || ThioBase || A database of thiopeptides featured in genetics and chemistry || GBrowse_syn || 2013
−
|
+
−
|http://projects.tcag.ca/xenodup/gbrowse.php
+
−
|
+
 
|-
 
|-
−
|OMAP
+
| http://dgv.tcag.ca/ || Database of Genomic Variants ||  || GBrowse || 2013
−
|Oryza Map Alignment Project
+
−
|http://www.omap.org/
+
−
|
+
 
|-
 
|-
−
|Oncorhynchus tshawytscha
+
| http://diagcomputing.org/resources/software.php || Data-Intensive Academic Grid || Provides a VM/cloud image of bioinf. software || JBrowse, BioMart, Ergatis, etc. || 2013
−
|Chinook salmon SAGE
+
−
|http://gmod.mbl.edu/perl/site/salmontrout
+
−
|
+
 
|-
 
|-
−
|OryGenesDB
+
| http://www.dictybase.org || [[:Category:DictyBase|DictyBase]] ||  || Chado, GBrowse, more || 2013
−
|
+
−
|http://orygenesdb.cirad.fr/
+
−
|
+
 
|-
 
|-
−
|Oryza Chromosome 8
+
| http://ecobrowser.biosino.org || EcoBrowser || E. coli transcriptome || JBrowse || 2013
−
|
+
−
|http://map.lab.nig.ac.jp/cgi-bin/gbrowse/Oryza_chr8/
+
−
|
+
 
|-
 
|-
−
|ParameciumDB
+
| http://ecocyc.org/ || EcoCyc ||  ||  || 2013
−
|
+
−
|http://paramecium.cgm.cnrs-gif.fr/
+
−
|Yes
+
 
|-
 
|-
−
|PeanutMap
+
| http://ecoliwiki.net || EcoliWiki || E. coli || || 2013
−
|
+
−
|http://peanutgenetics.tamu.edu/cmap/
+
−
|
+
 
|-
 
|-
−
|Philodina roseola
+
| http://www.endophyte.uky.edu/ || UKY Genome Projects || University of Kentucky; numerous spp || GBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/proseola
+
−
|
+
 
|-
 
|-
−
|PlantsDB
+
| 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
−
|MIPS PlantsDB
+
−
|http://mips.gsf.de/cgi-bin/proj/plant/gbrowse/synbrowse
+
−
|
+
 
|-
 
|-
−
|PlasmoDB
+
| http://www.equinegenome.org/ || Equine Genome || Equus caballus || GBrowse || 2013
−
|Plasmodium Genome Resource
+
−
|http://www.plasmodb.org/
+
−
|
+
 
|-
 
|-
−
|PossumBase
+
| 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://www.possumbase.org.nz/cgi-bin/gbrowse/mondom4/
+
−
|
+
 
|-
 
|-
−
|PseudoCAP
+
| http://fagaceae.org || Fagaceae Genomics Web || ''Fagaceae'' spp, including oak, beech, chestnut, etc. || Tripal || 2013
−
|Pseudomonas Genome Database
+
−
|http://v2.pseudomonas.com/whats_new.jsp
+
−
|
+
 
|-
 
|-
−
|PUMAdb
+
| http://www.flybase.org || [[:Category:FlyBase|FlyBase]] || A Database of Drosophila Genes & Genomes || Chado, GBrowse, more || 2013
−
|Princeton Microarray Database, Chado
+
−
|http://puma.princeton.edu/
+
−
|
+
 
|-
 
|-
−
|RGD
+
| https://www.cistrack.org/flynet/site/ || Flynet || CisTrack (Cis-regulatory Module Tracking) extension for Drosophila || JBrowse || 2013
−
|Rat Genome Database
+
−
|http://rgd.mcw.edu
+
−
|
+
 
|-
 
|-
−
|Schistosoma mansoni
+
| http://fungalgenomes.org/ || Fungal Genomes || Fungal Genomics Resources || || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/s_mansonigenome
+
−
|
+
 
|-
 
|-
−
|Schistosoma mansoni EST
+
| http://fungidb.org/ || FungiDB || Fungal Genomics Resources || || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/s_mansoniest
+
−
|
+
 
|-
 
|-
−
|SCRI Plant Bioinformatics Group
+
| http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/A_fumigatus_tigr_tel_100k || A. fumigatus TIGR/Sanger Assembly ||  ||  || 2013
−
|
+
−
|http://bioinf.scri.sari.ac.uk/
+
−
|Yes
+
 
|-
 
|-
−
|SGD
+
| http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/S_nodorum_broad_tel_100k || S. nodorum Fungal Telomere Browser ||  ||  || 2013
−
|
+
−
|http://db.yeastgenome.org/cgi-bin/gbrowse/scgenome/
+
−
|
+
 
|-
 
|-
−
|S. cerevisiae Proteome Browser
+
| http://fvgbrowse.agron.iastate.edu/ || ''Fusarium virguliforme'' Genome Browser || Soybean pathogen F. virguliforme || GBrowse || 2014
−
|
+
−
|http://db.yeastgenome.org/cgi-bin/gbrowse/scproteome/
+
−
|
+
 
|-
 
|-
−
|SGD Lite
+
| http://gabcsfl.org || Cool Season Food Legume Database || Cool season legumes, e.g. pea, lentil, chickpea, fava beans, etc. || Tripal || 2013
−
|
+
−
|http://sgdlite.princeton.edu/
+
−
|
+
 
|-
 
|-
−
|SmedDB
+
| http://gbrowse.csbio.unc.edu/cgi-bin/gb2/gbrowse/slep/ || Evidence Project Psychiatric Genetics || Human || GBrowse || 2013
−
|Planaria ESTs
+
−
|http://planaria.neuro.utah.edu/tools/tools.php
+
−
|Yes
+
 
|-
 
|-
−
|SOL Genomics Network
+
| http://gbrowse.jcvi.org/gbrowse/ || JCVI || J. Craig Venter Institute; offers numerous species || || 2013
−
|
+
−
|http://www.sgn.cornell.edu/
+
−
|Yes
+
 
|-
 
|-
−
|Soybase
+
| http://jcvi.org/medicago/ || JCVI || ''Medicago'' @ J. Craig Venter Institute || JBrowse, GBrowse, InterMine, Textpresso || 2014
−
|
+
−
|http://soybase.agron.iastate.edu/
+
−
|
+
 
|-
 
|-
−
|Soybean Gbrowse Database
+
| https://gdoc.georgetown.edu/gdoc/ || G-DOC || Systems medicine platform for personalized oncology || JBrowse || 2013
−
|
+
−
|http://soybeangenome.siu.edu/
+
−
|
+
 
|-
 
|-
−
|SpBase
+
| http://www.genedb.org || GeneDB || Pathogen Sequencing Unit || Chado, JBrowse || 2013
−
|
+
−
|
+
−
|
+
 
|-
 
|-
−
|Synechococcus 4320_2
+
| http://www.generationcp.org/ || Generation Challenge Programme || || || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/syn_4320_2
+
−
|
+
 
|-
 
|-
−
|Synechococcus CC9605
+
| http://genolab.inp-toulouse.fr/gb2/gbrowse/medic3/ || EcoLab @ INP Toulouse || Medicago || [http://genolab.inp-toulouse.fr/gb2/gbrowse/medic3/ GBrowse], [http://genolab.inp-toulouse.fr/cmap/ CMap] || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/syn_cc9605
+
−
|
+
 
|-
 
|-
−
|Synechococcus CC9902
+
| http://genome.igib.res.in/cgi-bin/gbrowse/AsianGenome/ || Asian Genome Browser || Human || GBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/syn_cc9902
+
−
|
+
 
|-
 
|-
−
|Synechococcus RS9916
+
| http://www.genome.ou.edu/ || Uni Oklahoma Advanced Center for Genome Technology || Various spp || GBrowse, JBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/syn_rs9916
+
−
|
+
 
|-
 
|-
−
|Synechococcus RS9917
+
| http://www.genome.ou.edu/tomato.html || Uni of Oklahoma tomato group || ''Solanaceae lycopersicum'' sequence || JBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/syn_rs9917
+
−
|
+
 
|-
 
|-
−
|Synechococcus WH5701
+
| http://genome.semo.edu/ || Southeast Fungal Biology Group || ''Coprinus'', ''Phanerochaete'' genome || GBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/syn_wh5701
+
−
|
+
 
|-
 
|-
−
|Synechococcus WH7805
+
| http://genomes.sapac.edu.au/bovineqtl/ || Bovine QTL Viewer || ''Bos taurus'' ||  || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/syn_wh7805
+
−
|
+
 
|-
 
|-
−
|T1DBase
+
| http://www.genomesunzipped.org/jbrowse/ || Genomes Unzipped || Human -- personal genomic data made public || JBrowse || 2013
−
|Type 1 Diabetes Database
+
−
|http://t1dbase.org/cgi-bin/dispatcher.cgi/Welcome/display
+
−
|
+
 
|-
 
|-
−
|TAIR
+
| http://genomics.research.iasma.it/ || Istituto Agrario S. Michele all'Adige bioinformatics resources || Apple, grape || GBrowse, CMap || 2013
−
|
+
−
|http://www.arabidopsis.org
+
−
|
+
 
|-
 
|-
−
|TGD
+
| http://genomsawit.mpob.gov.my/genomsawit/ || Malaysian Oil Palm Genome Program (MyOPGP) || Oil palm, ''Elaeis guineensis'' and ''E. oleifera'' || MAKER || 2014
−
|Tetrahymena Genome Database
+
|-
−
|http://www.ciliate.org/help/Locus.shtml
+
| http://www.genoscope.cns.fr/spip/Ressources-bioinformatiques-du.html || Genoscope || Multiple organisms || GBrowse || 2013
−
|
+
 
|-
 
|-
−
|TGI
+
| http://genexpdb.ou.edu/main/ || E. coli GenExpDB || E. coli Gene Expression Database || JBrowse || 2013
−
|The Gene Index Project
+
−
|http://biocomp.dfci.harvard.edu/tgi/
+
−
|
+
 
|-
 
|-
−
|TIGR
+
| http://ghost.zool.kyoto-u.ac.jp/cgi-bin/gb2/gbrowse/kh/ || Ghost Database || Ciona intestinalis genomic and cDNA resources || GBrowse || 2013
−
|The Institute for Genomic Research
+
−
|http://www.tigr.org
+
−
|Yes
+
 
|-
 
|-
−
|TIGR Medicago BACs
+
| http://giardiadb.org || GiardiaDB || Giardia (part of EupathDB) || || 2013
−
|
+
−
|http://www.tigr.org/tigr-scripts/medicago/gbrowse_bacs.pl
+
−
|
+
 
|-
 
|-
−
|TIGR Rice Genome Browser
+
| http://github.com/capsid || CaPSID || Computational Pathogen Sequence IDentification - open source platform for pathogen sequence identification || JBrowse || 2013
−
|
+
−
|http://rice.tigr.org/tigr-scripts/osa1/gbrowse/ricegenomebrowser
+
−
|
+
 
|-
 
|-
−
|ToxoDB
+
| http://gmod.mbl.edu/ || JBPC Generic Model Organism Database servers || Huge set of GMOD/GBrowse resources covering many different species ||  || 2013
−
|Toxoplasma gondii database
+
−
|http://v3-0.toxodb.org/
+
−
|
+
 
|-
 
|-
−
|TriAnnot BAC Viewer
+
| http://www.gnpannot.org/ || GNPannot || Community system of structural and functional annotation supported by comparative genomics<br>Produces [http://www.gnpannot.org/content/chado-controller Chado controller] || Chado, others || 2013
−
|
+
−
|http://urgi.infobiogen.fr/projects/TriAnnot/GBrowse.php
+
−
|
+
 
|-
 
|-
−
|Trypanosoma brucei brucei
+
| http://www.gramene.org || [[:Category:Gramene|Gramene]] || Grain resources ||  || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/t_bruceibrucei02
+
−
|
+
 
|-
 
|-
−
|Trypanosoma brucei brucei GenBank Entries
+
| http://green.dna.affrc.go.jp/Og/ || AfRicA DB || African Rice Annotation DataBase || GBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/t_bruceigenbank
+
−
|
+
 
|-
 
|-
−
|Trypanosoma brucei brucei RNA editing database
+
| http://gresource.hzau.edu.cn/resource/resource.html || GResource || Rice || GBrowse || 2014
−
|
+
−
|http://gmod.mbl.edu/gb/gbrowse/grna
+
−
|
+
 
|-
 
|-
−
|Trypanosoma brucei gambiense
+
| http://hapmap.ncbi.nlm.nih.gov/index.html.en || HapMap ||  ||  || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/t_bruceigambiense
+
−
|
+
 
|-
 
|-
−
|Trypanosoma brucei rhodesiense
+
| http://www.hardwoodgenomics.org || Hardwood Genomics Project || Hardwood tree spp || Tripal || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/t_bruceirhodesiense
+
−
|
+
 
|-
 
|-
−
|Trypanosoma cruzi
+
| http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/ || Human Genome Diversity Project || HGDP @ [http://pritch.bsd.uchicago.edu/ Pritchard lab, UChicago] || GBrowse || 2013
−
|
+
−
|http://gmod.mbl.edu/perl/site/t_cruzi
+
−
|
+
 
|-
 
|-
−
|UNH HCGS Tetraodon Genome Browser
+
| 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
−
|Gbrowse plus GFF
+
−
|http://hcgs.unh.edu/gbrowse/
+
−
|
+
 
|-
 
|-
−
|VectorBase
+
| http://huref.nimbusinformatics.com/ || HuRef Genome Project || Human Ref Genome Project || JBrowse || 2013
−
|Chado, DAS, Apollo
+
−
|http://www.vectorbase.org
+
−
|Yes
+
 
|-
 
|-
−
|Vicogenta
+
| http://hymenopteragenome.org/beebase/ || BeeBase || The secret life of bees || JBrowse || 2013
−
|Viewer for Comparing Genomes to Arabidopsis
+
−
|http://nypg.bio.nyu.edu/vicogenta/
+
−
|
+
 
|-
 
|-
−
|wFleaBase
+
| http://hymenopteragenome.org/ant_genomes/ || Ant Genomes Portal || Ants || GBrowse || 2013
−
|Daphnia
+
−
|http://wfleabase.org/
+
−
|Yes
+
 
|-
 
|-
−
|WormBase
+
| http://hymenopteragenome.org/nasonia/ || NasoniaBase || Nasonia wasp || GBrowse || 2013
−
|
+
−
|http://www.wormbase.org
+
−
|
+
 
|-
 
|-
−
|XanthusBase
+
| http://icemangenome.net/ || Ice Man Genome || The genome of Ötzi the Iceman || JBrowse || 2013
−
|
+
−
|http://www.xanthusbase.org/
+
−
|Yes
+
 
|-
 
|-
−
|Xenbase
+
| http://ich.ciliate.org/ || IchDB || Ichthyophthirius multifiliis genome || || 2013
−
|
+
−
|http://www.xenbase.org/
+
−
|
+
 
|-
 
|-
−
|
+
| http://cmap.icrisat.ac.in/cmap/index_public.html || <abbr title="International Crops Research Institute for the Semi-Arid Tropics">ICRISAT</abbr> India ||  || CMap || 2013
−
|Trichomona vaginalis
+
−
|http://www.uclaaccess.ucla.edu/UCLAACCESS/Web/Faculty.aspx?ri=58
+
−
|Yes
+
 
|-
 
|-
−
|
+
| http://www.icugi.org || Cucurbit Genomics Database || Cucumbers, melons, squashes || GBrowse, CMap || 2013
−
|Microarray data, Chado, H. sapiens
+
−
|http://genetics.ucla.edu/labs/nelson/
+
−
|Yes
+
 
|-
 
|-
−
|
+
| http://www.imm.ox.ac.uk/mrc-molecular-haematology-unit || Genome Biology Group @ [http://www.imm.ox.ac.uk/ Weatherall Institute of Molecular Medicine] || [https://gbrowse2.molbiol.ox.ac.uk/gbrowse2/MM9_CapC_erythroid/capc_full.html example] || GBrowse || 2014
−
|
+
−
|http://www.wicell.org
+
−
|Yes
+
 
|-
 
|-
 +
| 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
 +
<!-- |-
 +
X | http://maizeapache.ddpsc.org/cgi-bin/gbrowse.cgi?source=01_azm2bac || AZM-to-BAC Viewer ||  ||  || 200x
 +
|-
 +
X | http://maizeapache.ddpsc.org/cgi-bin/gbrowse.cgi?source=02_azm2gene || AZM-to-Gene Viewer ||  ||  || 200x
 +
|-
 +
X | http://map.lab.nig.ac.jp/cgi-bin/gbrowse/Oryza_chr8/ || Oryza Chromosome 8 ||  ||  || 200x
 +
-->
 +
|-
 +
| 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 <ref name="DOI:10.1093/pcp/pct157" /> || 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'' <ref name="DOI:10.1186/1471-2164-14-741" /> || 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
 +
<!-- not sure this is still running!
 +
|-
 +
| 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 || 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
 +
 +
<!--
 +
|-
 +
X | http://projects.tcag.ca/cgi-bin/duplication/dupbrowse/human_b36 || Human Genome Segmental Duplication Database ||  ||  || 200x
 +
|-
 +
X | http://projects.tcag.ca/xenodup/gbrowse.php || Non-Human Segmental Duplication Database ||  || ||
 +
-->
 +
|-
 +
| 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
 +
<!-- ??? still using Chado?
 +
|-
 +
| 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 ||  || 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 || <abbr title="South African National Bioinformatics Institute">SANBI</abbr> || T. brucei || || 2013
 +
|-
 +
| http://seacow.helmholtz-muenchen.de/cgi-bin/gb2/gbrowse/Barley_PhysMap/ || TriticeaeGenome || Barley at <abbr title="Munich Information Centre for Protein Sequence">MIPS</abbr> || 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/ || [[:Category:SGN|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 [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://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 <abbr title="Database Centre for Life Science">[http://dbcls.rois.ac.jp/ DBCLS]</abbr> || 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 <ref name="DOI:10.1371/journal.pone.0075265" /> || ''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 [http://www.cirad.fr/ 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 || [[:Category:WormBase|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/|| [[:Category:SGD|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 <ref name="doi:10.1093/molbev/msu139" /> || retrocopies || JBrowse || 2014
 +
|-
 +
| http://ngspipelines.toulouse.inra.fr:9019 || NGS Pipelines || SeaBass brain and liver transcriptome || BioMart; JBrowse || 2014
 +
|-
 +
| http://sigenae.org || <abbr title="Information Systems of Analysis of Breeding Animals’ Genome program (in French)">Sigenae</abbr> || 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 <ref name="doi:10.1186/1471-2164-15-308" /> || ''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
 
|}
 
|}
  
 +
<references />
 +
<!--
 
==GBrowse Users==
 
==GBrowse Users==
  
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* Agricultural Biotechnology Center, Hungary
 
* Agricultural Biotechnology Center, Hungary
 +
* AphidBase
 
* BAWI, S. Korea
 
* BAWI, S. Korea
 
* Baylor College of Medicine
 
* Baylor College of Medicine
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* CSIRO, Australia
 
* CSIRO, Australia
 
* Cambridge University (multiple labs)
 
* Cambridge University (multiple labs)
−
* Center for Genomics & Bioinformatics, Stockholm
 
 
* Center for Genomics and Bioinformatics, Stockholm
 
* Center for Genomics and Bioinformatics, Stockholm
 
* Centre de Genetique Moleculaire, CNRS
 
* Centre de Genetique Moleculaire, CNRS
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* EuGenes (hacked copy)
 
* EuGenes (hacked copy)
 
* Faculdade de Medicina de Ribeiro Preto, So Paulo
 
* Faculdade de Medicina de Ribeiro Preto, So Paulo
−
* FlyBase
+
* Family Tree DNA, Genealogy by Genetics Ltd.
 
* Foundation for Research and Technology, Crete
 
* Foundation for Research and Technology, Crete
 
* Fundao Hemocentro, Sao Paolo
 
* Fundao Hemocentro, Sao Paolo
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* Meat Animal Research Center, University of Nebraska
 
* Meat Animal Research Center, University of Nebraska
 
* Medical University of South Carolina
 
* Medical University of South Carolina
−
* Michigan State University  
+
* Michigan State University
 
* NHGRI, NIH
 
* NHGRI, NIH
 
* National Cancer Institute, Frederick Cancer Center
 
* National Cancer Institute, Frederick Cancer Center
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* QIAGEN Operon Corp.
 
* QIAGEN Operon Corp.
 
* RIKEN (multiple labs)
 
* RIKEN (multiple labs)
−
* RatDB
 
 
* Regulome, Inc.
 
* Regulome, Inc.
 
* Rhobio (Bayer CropScience SA & Biogemma joint venture)
 
* Rhobio (Bayer CropScience SA & Biogemma joint venture)
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* Stowers Institute for Medical Research
 
* Stowers Institute for Medical Research
 
* Texas A&M (multiple labs)
 
* Texas A&M (multiple labs)
 +
* [http://txbiomed.org Texas Biomedical Research Institute]
 
* The Institute for Genome Research
 
* The Institute for Genome Research
−
* Tulane University
 
 
* Tulane University
 
* Tulane University
 
* University California Davis
 
* University California Davis
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* Wageningen Universiteit & Researchcentrum, Netherlands
 
* Wageningen Universiteit & Researchcentrum, Netherlands
 
* Washington University at St. Louis (multiple labs)
 
* Washington University at St. Louis (multiple labs)
−
* WormBase
 
 
* deVGen, Belgium
 
* deVGen, Belgium
 +
-->
 +
 +
[[Category:Users]]

Latest revision as of 10:43, 12 August 2014

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
  1. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0079909
  2. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0086318
  3. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1093.2Fpcp.2Fpct157
  4. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1186.2F1471-2164-14-741
  5. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0075265
  6. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named doi:10.1093.2Fmolbev.2Fmsu139
  7. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named doi:10.1186.2F1471-2164-15-308
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