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Created on: 26-Oct-2012   Last updated on: 26-Oct-2012  |  How to cite this?
Total resources - 108
A list of resources for genomes and genomics
Akhilesh Bajpai and Sravanthi Davuluri (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources
Short description*Rank by usage frequency Click to Edit / Add comments
Ensembl
http://www.ensembl.org
A web resource for genome assemblies, sequences and their annotations
38
GOLD - Genomes Online Database
http://www.genomesonline.org
A web resource for information on genome and metagenome sequencing projects, and their associated metadata
50
1000 Genomes - A Deep Catalog of Human Genetic Variation
http://www.1000genomes.org
Genomes of a large number of human population
52
FlyBase - A Database of Drosophila Genes & Genomes
http://flybase.org
A database and web portal for genetic and genomic information on the fruit fly Drosophila melanogaster and related fly species
75
MGI - Mouse Genome Informatics
http://www.informatics.jax.org
An international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data
78
HIV databases
http://www.hiv.lanl.gov
A database on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials
81
JGI Genome Portal
http://genome.jgi-psf.org
A comprehensive genome portal for multiple organisms and species
87
IMG - Integrated Microbial Genomes
http://img.jgi.doe.gov
A comprehensive resource for annotation and analysis of genome and metagenome datasets
89
CMR - Comprehensive Microbial Resource
http://cmr.jcvi.org
A comprehensive microbial resource for information on all of the publicly available, complete prokaryotic genomes
90
CGD - Candida Genome Database
http://www.candidagenome.org
A resource for genomic sequence and gene and protein information for Candida albicans
92
GRAMENE
http://www.gramene.org
A comprehensive resource for comparative grass genomics
92
MaizeGDB - Maize Genetics and Genomics Database
http://www.maizegdb.org
A repository for maize sequence, phenotype, stock, genotypic and karyotypic variation, and chromosomal mapping data
94
Medicago truncatula - A model for legume research
http://www.medicago.org
A collection of Medicago truncatula related resources including genomes
96
BioCyc
http://biocyc.org
A collection of databases describing the genome and metabolic pathways of many organisms.
97
GDR - Genome Database for Rosaceae
http://www.rosaceae.org
A curated and integrated database for centralized access to Rosaceae genomics and genetics data with analysis tools
97
Animal Genome Size Database
http://www.genomesize.com
A comprehensive catalog of haploid genomes from various animal species
98
AspGD - Aspergillus Genome Database
http://www.aspgd.org
An online resource that contains genetic and molecular biological information about Aspergillus
98
Cucurbit Genomics Database
http://www.icugi.org
A resource for Cucurbit species, including sequence data and tools for analysis
98
CyanoBase
http://genome.kazusa.or.jp/cyanobase
A resource for sequences and annotation data on the structures of the cyanobacterial genomes
98
Dendrome - A Forest Tree Genome Database
http://dendrome.ucdavis.edu
A database for forest tree genome data and related information
98
dictyBase
http://dictybase.org/
A central resource for Dictyostelid genomics
98
GrainGenes - A Database for Triticeae and Avena
http://wheat.pw.usda.gov/GG2
A suite for the Triticeae and Oat research, including databases, tools, data files, etc.
98
Amborella Genome Database
http://www.amborella.org
A genomics resource of Amborella trichopoda
99
BDGP - Berkeley Drosophila Genome Project
http://www.bdgp.org
A consortium of the Drosophila Genome Center providing sequences, materials, methods, and software
99
CGD - Cacao Genome Database
http://www.cacaogenomedb.org
A database that contain annotated EST databases of cacao, maps and markers, all publicly available sequences and the raw and assembled output of the ongoing cacao genome sequencing project
99
EBI Genomes
http://www.ebi.ac.uk/genomes
A database from EBI for genomes of various organisms
99
FungiDB - Fungi Genomics Resources
http://fungidb.org
A comprehensive genomics and functional resource for fungal species
99
GeneDB
http://www.genedb.org
A comprehensive resource for the sequence and annotation data for several pathogens
99
MBGD - Microbial Genome Database
http://mbgd.genome.ad.jp
A database for comparative analysis of completely sequenced microbial genomes by ortholog identification, paralog clustering, motif analysis and gene order comparison
99
AGD - Ashbya Genome Database
http://agd.vital-it.ch
A genome/transcriptome database with gene annotation and microarray expression data from Ashbya gossypii and Saccharomyces cerevisiae.
100
Animal Genome Database
http://animal.dna.affrc.go.jp
A resource for swine (Sus scrofa) genomics
100
AphidBase
http://www.aphidbase.com
A database for Aphid genome
100
Avian Genomes
http://aviangenomes.org
A comprehensive functional genomics resource for the genome and transcriptome of avian species
100
BacMap Genome Atlas
http://wishart.biology.ualberta.ca/BacMap  http://bacmap.wishartlab.com 
An interactive database for bacterial genomes
100
BeeBase
http://hymenopteragenome.org/beebase
A comprehensive resource for sequence data for the bee research
100
BGD - Bovine Genome Database
http://bovinegenome.org
A resource with integrated tools for Bos taurus genome
100
BioBIKE
biobike.csbc.vcu.edu
A bioligical integrated knowledge environment, which provides information on genomic sequences, gene annotations, functional descriptions, formal categories and hierarchical groups of metabolic reactions with genes.
100
BROAD Institute Genome data
http://www.broadinstitute.org/scientific-community/data
Genomes for multiple organism and species
100
Burkholderia Genome Database
http://www.burkholderia.com
A resource for updated annotations and comparative analysis of Burkholderia genomes
100
Castor Bean Genome Database
http://castorbean.jcvi.org
A database for castor bean (Ricinus communis) genomics
100
Catfish Genome Database - cBARBEL
http://www.catfishgenome.org/cbarbel
A resource for genetics and genomics research of Ictalurid catfish
100

URL not working as on 14 Nov 2016 (confirmed on 23 Feb 2017)
CHO Genome - Chinese Hamster Genome Database
http://www.chogenome.org
A resource for CHO cell genomics
100
Citrus Genome Database
http://www.citrusgenomedb.org
A resource for Citrus genomics, genetics, breeding, and tools for analysis
100
coliBASE - a genome resource for the E. coli research community
http://www.xbase.ac.uk/colibase
A comprehensive resource for comparative bacterial genomics, with multiple genomes
100
CottonDB - Cotton Genome Database
http://www.cottondb.org
A database with genomic, genetic and taxonomic information for cotton
100

Website states that the database has been moved to a new server since October 2011 and is in preparation for its conversion to a new database- CottonGen
Cucumber Genome DataBase
http://cucumber.genomics.org.cn/page/cucumber/index.jsp
A database of Cucumber genome and related information
100
CYGD - Comprehensive Yeast Genome Database
http://mips.helmholtz-muenchen.de/genre/proj/yeast
A database that provides sequence information and functional annotations on individual genes and proteins of yeast
100
Eucalyptus camaldulensis Genome Database
http://www.kazusa.or.jp/eucaly
Genetic information, investigated by sequencing the genome and the cDNA
100
FGDB - Fusarium graminearum Genome Database
http://mips.helmholtz-muenchen.de/genre/proj/fusarium
A resource for information on filamentous fungus Fusarium graminearum genome molecular structure and functional network
100
GENOME 10KŪ - Unveiling animal diversity
http://genome10k.soe.ucsc.edu
A resource of DNA sequences representing the genomes of 10,000 vertebrate species
100
GenomeAtlas
http://www.cbs.dtu.dk/services/GenomeAtlas
A database for sequence data and bioinformatics results
100
Genomes Unzipped - public personal genomics
http://www.genomesunzipped.org
A blog that provides expert commentary on the personal genomics industry, including genomic data and browser
100
GenomeWeb - Lists of Genome Sites
http://www.biologie.uni-hamburg.de/b-online/library/genomeweb/GenomeWeb/prokaryote-gen-db.html
A collection of prokaryotic genome databases
100
GNN - Genome News Network
http://www.genomenewsnetwork.org
An online magazine that covers important developments in genomics research around the world
100
GOBASE - an organelle genome database
http://gobase.bcm.umontreal.ca
A organelle genome database that integrates diverse data related to mitochondria and chloroplasts
100
Heliconius Genome Project
http://www.butterflygenome.org
A web-portal for the Heliconius butterfly genome project
100
HGD - Hymenoptera Genome Database
http://hymenopteragenome.org
A database of the genomes of bees Apis mellifera, Bombus terrestris and B. impatiens, the parasitoid wasp Nasonia vitripennis, and few species of ants
100
Jatropha Genome Database
http://www.kazusa.or.jp/jatropha
A resource for genomics analysis of Jatropha
100
JGI Genome Channel
http://compbio.ornl.gov/channel
A resource with integrated tools for the microbial genomes sequenced by the Joint Genome Institute (JGI)
100
KEGG GENOME Database
http://www.genome.jp/kegg/genome.html
A collection of KEGG organisms with known complete genome sequences
100
MicrobesOnline
http://www.microbesonline.org
A resource for microbial comparative and functional genomics analysis, and includes genomes and expression data for various microbial species
100
Microbial Genomics
http://microbialgenomics.energy.gov/databases.shtml
A site providing web-based resources for microbial genomics
100
MicroScope - Microbial Genome Annotation & Analysis Platform
https://www.genoscope.cns.fr/agc/microscope
A resource for microbial genome annotation and functional analysis
100
MIPS - PlantsDB
http://mips.helmholtz-muenchen.de/plant/genomes.jsp
An integrated platform for comparative plant genome research
100
MITOMAP
http://www.mitomap.org/MITOMAP
A human mitochondrial genome database
100
miyakogusa.jp
http://www.kazusa.or.jp/lotus
A resource for structural features of the Lotus japonicus genome
100
Mouse Genomes Project
http://www.sanger.ac.uk/resources/mouse/genomes
Genomics data and related information for several mouse strains
100
MPGDB - Mycobacteriophage Genome DataBase
http://mpgdb.ibioinformatics.org/mpgdb.php
A resource that provides detailed information on genes and proteins of mycobacteriophages sequenced completely
100
MycoCosm - the fungal genomics resource
http://genome.jgi.doe.gov/programs/fungi
A comprehensive functional genomics portal for fungal species
100
NCBI Genome
http://www.ncbi.nlm.nih.gov/genome
A resource that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations
100
NIG Mouse Genome Database
http://molossinus.lab.nig.ac.jp/msmdb
A mouse genome database from National Institute of Genetics
100
ParameciumDB
http://paramecium.cgm.cnrs-gif.fr
An integrated database and analysis platform for the Model Organism Paramecium tetraurelia
100
PlantGDB
http://www.plantgdb.org
A resource providing sequence data and custom EST assemblies (PUT) for various plant species as well as web tools and plant genome browsers
100
PlasmoDB - Plasmodium Genomics Resource
http://plasmodb.org/plasmo
A database of Plasmodium with information on annotated genomes, evidence of transcription, proteomics evidence etc. and tools for data analysis and visualization
100
PomBase
http://www.pombase.org
A database for Schizosaccharomyces pombe providing structural and functional sequence annotation and access to large-scale data sets
100
PopulusDB
http://www.populus.db.umu.se
A comprehensive resource for tree genomics
100
Pseudomonas Genome Database
http://www.pseudomonas.com
A resource for the Pseudomonas aeruginosa PAO1 reference strain's genome and comparative analyses of several related Pseudomonas species.
100
Pythium Genome Database
http://pythium.plantbiology.msu.edu
A resource for Phytopathogen (Pythium ultimum) genome
100
RCGDB - Roche Cancer Genome Database
http://rcgdb.bioinf.uni-sb.de/MutomeWeb
A cancer genome database from Roche
100
RGD - Rat Genome Database
http://rgd.mcw.edu
A database that provides information on rat genomes, diseases, phenotypes, models and also various genome analysis tools
100
RicBase - Rickettsia Genome Database
http://igs-server.cnrs-mrs.fr/mgdb/Rickettsia
A resource for genomes of different species of Rickettsia
100
Rice Genome Annotation Project Database
http://rice.plantbiology.msu.edu
A resource with integrated analysis tools for sequence and annotation data for the rice genome
100
SGD - Saccharomyces Genome Database
http://www.yeastgenome.org
A comprehensive resource that provides integrated biological information for the budding yeast Saccharomyces cerevisiae and various search and analysis tools
100
SGD - Sugi Genome Database
http://www.ffpri.affrc.go.jp/labs/cjgenome
A genome database of Cryptomeria japonica
100
Silencing Genomes
http://www.silencinggenomes.org
A resource on C. elegans gene silencing and related information
100
SilkDB - Silkworm Genome Database
http://silkworm.genomics.org.cn
A database that provides genomic data including functional annotation of genes, gene products and chromosomal mapping for the Bombyx mori
100
SmedGD - Schmidtea mediterranea Genome Database
http://smedgd.neuro.utah.edu
An integrated database for planarian genome, including predicted and annotated genes, ESTs, protein homologies, etc.
100
sol genomics network
http://solgenomics.net
A resource with integrated tools for Solanum and Nicotiana species genomes
100
SoyBase
http://www.soybase.org
An integrated genomics and molecular biology platform for Soybean research
100
Soybean GBrowse Database
http://soybeangenome.siu.edu
An integrative visualization of soybean genomic features
100
StellaBase - Nematostella vectensis Genomics Database
http://nematostella.bu.edu/stellabase
A genomics database for Nematostella vectensis
100
TAIR - The Arabidopsis Information Resource
http://www.arabidopsis.org
A resource for the model plant Arabidopsis thaliana, providing complete genome sequence along with other information such as gene structure, metabolism, gene expression, genome maps, genetic markers
100
TB Database - An integrated platform for tuberculosis research
http://genome.tbdb.org
A comprehensive database including genomic data related to tuberculosis, with integrated tools for the analysis
100
TCGA - The Cancer Genome Atlas
http://cancergenome.nih.gov
A resource and analysis platform for the genomic data generated by TCGA
100
TGD wiki - Tetrahymena Genome Database wiki
http://ciliate.org
A user-updatable database of Tetrahymena thermophila genome sequence
100
The SEED Viewer
http://seed-viewer.theseed.org
A resource for curated data with comparative analysis and annotation of multiple genomes
100
TomDB - Tomato genome DataBase
http://mips.helmholtz-muenchen.de/plant/tomato/index.jsp
A database for tomato genome sequence
100
TriTrypDB - Kinetoplastid Genomics Resource
http://tritrypdb.org/tritrypdb
A comprehensive genomics and functional resource for Trypanosomatidae
100
UCSC Genome Browser
http://genome.ucsc.edu
A resource that contains the reference sequence and working draft assemblies for a large collection of genomes
100
USDA Public Citrus Genome Database
http://citrus.pw.usda.gov
A public citrus genome database
100
VectorBase
http://www.vectorbase.org
A resource for invertebrate vectors of human pathogens, including sequence data and tools for analysis
100
VEGA - Vertebrate Genome Annotation
http://vega.sanger.ac.uk
A repository for high quality manual annotation of vertebrate genome sequence
100
Virology.ca - Viral Bioinformatics Resource Center
http://athena.bioc.uvic.ca
A comprehensive portal for viral genomes data and analysis
100
VISTA - Tools for Comparative Genomics
http://genome.lbl.gov/vista
A comprehensive platform for comparative analysis of genomic sequences
100
wFleaBase - Daphnia Water Flea Genome Database
http://wfleabase.org
A resource for the Daphnia (water flea) species gene and genomics information
100
WormBase - Nematode Information Resource
http://www.wormbase.org
A resource with integrated tools for multiple worms genomics
100
Xenbase
http://www.xenbase.org
A comprehensive resource for Xenopus laevis and Xenopus tropicalis genomics
100
ZFIN - The Zebrafish Model Organism Database
http://zfin.org
A community resource of zebrafish genetic, genomic and developmental research information
100
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