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Archaeal Databases

Ensembl A browser for archaeal genomes https://bacteria.ensembl.org/index.html
EZ cloud EZ cloud for archaea http://www.ezbiocloud.net/ezgenome
IMG Integrated microbial genomes and microbiomes https://img.jgi.doe.gov/
MicrobesOnline resource A collection of 3707 microbial genomes http://www.microbesonline.org/
BacDive The bacterial diversity metadatabase contains detailed information on more than 20,000 strains of bacteria
https://bacdive.dsmz.de/
Wikipedia List of sequenced archaeal genomes https://en.wikipedia.org/wiki/List_of_sequenced_archaeal_ genomes UCSC archaeal genome browser Integrated genome browser for archaeal genomes http://archaea.ucsc.edu/

Bacterial Databases
Ensembl bacteria A browser for bacterial and archaeal genomes https://bacteria.ensembl.org/index.html

MBGD Database for comparative analysis of completely sequenced microbial genomes http://mbgd.genome.ad.jp/
Human microbiome project Characterisation of microbes in healthy humans https://hmpdacc.org/

GOLD Genomes online database https://gold.jgi.doe.gov/

EZ cloud EZ cloud for bacteria http://www.ezbiocloud.net/ezgenome

IMG Integrated microbial genomes and microbiomes https://img.jgi.doe.gov/
MicrobesOnline resource A collection of 3707 mmicrobial genomes http://www.microbesonline.org/

BacDive The bacterial diversity metadatabase contains detailed information on more than 20,000 strains of bacteria
https://bacdive.dsmz.de/
BIGSdb Bacterial isolate genome sequence database https://bigsdb.readthedocs.io/en/latest/
metaMicrobesOnline Website for browsing and comparing the genomes of 3527 microbial genomes
http://meta.microbesonline.org/
MetaRef A pan-genomic database for comparative and community microbial genomics

 https://omictools.com/metaref-tool
MetaBioME database MetaBioME is a web resource to find novel homologs for known commercially useful enzymes (CUEs) in metagenomic datasets and completed bacterial genomes

https://metasystems.riken.jp/metabiome/
PATRIC Pathosystems resource integration center https://www.patricbrc.org/
TBDB Tuberculosis database integrates genomic sequences and data for Mycobacterium species relevant to drug
discovery, vaccines, and biomarkers http://www.tbdb.org/
EuPathDB Eukaryotic pathogen database resources is a collection of individual databases, each focusing on specific pathogens, accessible through a common portal https://eupathdb.org/
coliBase A database for E. coli, Salmonella and Shigella http://xbase.warwick.ac.uk/colibase/
DEG Database of essential genes from bacteria and yeast http://www.essentialgene.org
Essential genes in E. coli First results of an E. coli gene deletion project

http://www.genome.wisc.edu/resources/essential.htm
GenoBase Escherichia coli K-12 in-frame, single gene knockout mutants http://ecoli.naist.jp/
HGT-DB Horizantal gene transfer database is a genomics database that includes G+C content, codon and amino-acid usage, as well as information on which genes deviate in these parameters for prokaryotic complete genomes
http://genomes.urv.es/HGT-DB/
Pseudomonas genome database Consists of information about Pseudomonas genome
http://www.pseudomonas.com/
PAIDB Pathogeneticity islands database http://www.paidb.re.kr/about_paidb.php

Plant Genome Databases
AgBase A curated, open-source, web-accessible resource for functional analysis of agricultural plant and animal gene products http://www.agbase.msstate.edu/
autoSNPdb Plant SNP discovery database http://autosnpdb.appliedbioinformatics.com.au/
BarleyBase Database for barley microarrays holds the data for over 1000 hybridizations from the affymetrix Barley1 GeneChip and genome arrays http://www.barleybase.org/
Cereal small RNA database An integrated resource for small RNAs such as miRNAs, siRNAs, ta-siRNAs
expressed in rice and maize http://sundarlab.ucdavis.edu/mrnas/
CR-EST Crop EST database https://apex.ipk-gatersleben.de/ apex/f?p¼116:1
EURISCO European catalogue for plant genetic resources http://eurisco.ecpgr.org/
GABiPD Genome analysis of the plant biological system http://www.gabipd.org/
GoMapMan Unified plant-specific gene ontology http://www.gomapman.org
GrainGenes Molecular and phenotypic information on grain yielding plants such as wheat,
barley, rye, triticale, and oats http://wheat.pw.usda.gov/

GreeNC Green non-coding database (GreeNC) is a repository of long non-coding RNAs annotated in 37 plant species and six algae http://greenc.sciencedesigners.com/wiki/Main_Page
MIPS plants database Plant database resource for integrative and comparative plant genome research
http://mips.gsf.de/proj/plant/jsf/
NIAS Databases for plant genetic resources and plant disease information http://www.gene.affrc.go.jp/databases_en.php

P-MITE Database of plant miniature inverted[1]repeat transposable elements (MITEs) http://pmite.hzau.edu.cn/django/mite/
PGDD A plant genome duplication database http://chibba.agtec.uga.edu/duplication/
Phytozome A database for green plant genomics http://www.phytozome.net/
PIECE Database of plant intron exon comparison and evolution
https://wheat.pw.usda.gov/piece/
Plant DNA C-values database A database that provides a one-stop, user riendly database where the plant genome
sizes can be readily accessed and compared http://www.kew.org/genomesize/homepage.html
Plant ontology database This database is a collection of plant systematics, botany and genomics involved in developing simple and controlled vocabularies that accurately reflect the biology of plant structures
http://www.plantontology.org/
Plant SnoRNA database A database of snoRNA genes in plant species
http://bioinf.scri.sari.ac.uk/cgi[1]bin/plant_snorna/home
Plant stress esponsive gene catalog Stress-responsive gene in various plant species http://dayhoff.generationcp.org/
Plant GDB A database of plant genomic sequences and ESTs http://www.plantgdb.org/
Plant PAN Plant promoter analysis navigator database http://PlantPAN2.itps.ncku.edu.tw
PlantProm A database of plant promoter sequences http://www.epd.isb-sib.ch/
PlantsP/ PlantsT PlantsP and PlantsT are plant-specific curated databases that combine sequence
derived information with experimental functional genomics data http://plantsp.sdsc.edu/
Plant tribes Families of protein-coding genes from five sequenced plant species

http://fgp.huck.psu.edu/tribedb/index.pl
PlantTFDB Plant transcription factor database provides a comprehensive, high-quality resource of plant transcription factors, regulatory elements and interactions between them http://planttfdb.cbi.pku.edu.cn
PLAZA A plant-oriented online resource for comparative, evolutionary and functional genomics
https://bioinformatics.psb.ugent.be/plaza

PMDBase A database of plant microsatellites and marker development http://www.sesame-bioinfo.org/PMDBase
TIGR database Plant transcript assemblies database http://plantta.tigr.org/
TROPGene A database comprising of genetic and genomic information about tropical crops such as banana, coconut, cotton, cocoa, etc. http://tropgenedb.cirad.fr/
ForestTree A resource that centralizes large-scale http://foresttree.org/ftdb
DataBase EST sequencing results from several tree species LegumelIP Model legumes integrative database
platform http://plantgrn.noble.org/LegumeIP/

Virus Databases

CoVDB Coronavirus genes and genomes http://covdb.microbiology.hku.hk/
DPV web Central source of information about viruses, viroids and satellites of plants, fungi, and protozoa http://www.dpvweb.net/
euHCVdb  European hepatitis C virus database  http://euhcvdb.ibcp.fr/
HCV database Hepatitis C virus database  http://hcv.lanl.gov/
HERVd  Human endogenous retrovirus database  http://herv.img.cas.cz/
HFV database Hemorrhagic fever virus sequence database http://hfv.lanl.gov/
HIV drug resistance DB Compilation of mutations in HIV genes that confer resistance to anti-HIV drugs
http://www.hiv.lanl.gov/content/sequence/RESDB/

Influenza research DB Influenza virus http://www.fludb.org

NCBI viral genomes Viral genomes resource http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html
Papillomavirus episteme A database of Papillomaviridae family of viruses http://PaVE.niaid.nih.gov
phiSITE Gene regulation in bacteriophages http://www.phisite.org
Poxvirus.org Poxvirus genomic sequences and gene annotation http://www.poxvirus.org/
VBRC Viral bioinformatics resource center http://www.biovirus.org/
ViTa microRNAs targets of the influenza virus http://vita.mbc.nctu.edu.tw/
ViralZone Molecular and epidemiological information on viral genera and families
http://viralzone.expasy.org/
ViralGenomes Viral sequence data resource by NCBI https://www.ncbi.nlm.nih.gov/genome/viruses/

Cell Organelle Databases

Chloroplast genome database Chloroplast genome http://chloroplast.cbio.psu.edu/
OrganelleDB A web-accessible database cataloging proteins localized to a known organelle
http://organelledb.lsi.umich.edu/
Organelle genomes Organelle genome resource at NCBI

 www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html
Plant organelles database Images of plant organelles and protocols for plant organelle research
http://podb.nibb.ac.jp/Organellome/
PLProt Arabidopsis thaliana chloroplast protein database http://www.plprot.ethz.ch/
Plastid-LCG base Plastid lineage-based conserved gene air database
http://lcgbase.big.ac.cn/plastidLCGbase/
HMPD Human mitochondrial protein database http://bioinfo.nist.gov/hmpd/
HmtDB Human mitochondrial DataBase http://www.hmtdb.uniba.it/
MamMiBase Database of complete mitochondrial genome sequences of over 100 mammalian species
http://www.mammibase.lncc.br/
MitoCarta Mouse and human mitochondrial proteins http://www.broadinstitute.org/pubs/MitoCarta
MitoDrome Annotating D. melanogaster nuclear genes encoding mitochondrial proteins and support studies on human diseases related to mitochondrial dysfunctions http://mitodrome.ba.itb.cnr.it/
MitoPorteome Mitochondrial protein sequences encoded by mitochondrial and nuclear genes
http://www.mitoproteome.org/
OGRe Database containing information on completely sequenced animal mitochondrial genomes of 473 species
http://ogre.mcmaster.ca/

Arabidopsis mitochondrial protein database Database comprising of experimentally identified proteins in Arabidopsis mitochondrial genome www.plantenergy.uwa.edu.au/applications/ampdb/index.html

n-Vertebrate Genome Databases

AphidBase Genome database of pea aphid (Acyrthosiphon pisum) http://www.aphidbase.com/
AppaDB Database of nematode Pristionchus pacificus http://appadb.eb.tuebingen.mpg.de
BeetleBase Database of the beetle Tribolium castaneum http://www.beetlebase.org
CeNDR C. elegans natural diversity resource http://www.elegansvariation.org

Comparasite Database for comparative studies of transcriptomes of parasites http://comparasite.hgc.jp/
CuticleDB Structural proteins of arthropod cuticle http://bioinformatics.biol.uoa.gr/cuticleDB/
FlyBrain Database of drosophila nervous system http://flybrain.neurobio.arizona.edu/Helminth.net

Parasitic nematode sequencing project http://www.helminth.net
InsectBase Insect genomes and transcriptomes http://www.insect-genome.com/
Hymenoptera genome Genome sequences and annotation for honey bee and the parasitoid wasp
Nasonia vitripennis http://HymenopteraGenome.org
InsectBase Insect genomes and transcriptomes http://www.insect-genome.com/
SilksatDB Comprehensive relational database of silkworm microsatellite

 http://www.cdfd.org.in/SILKSAT/index.php
SpodoBase Genomics of the butterfly Spodoptera frugiperda http://bioweb.ensam.inra.fr/spodobase/
VectorBase Invertebrate vectors of human pathogens http://www.vectorbase.org
RNAiDB RNAi phenotypic analysis of C. elegans genes http://www.rnai.org/
NEMBASE Nematode sequence and functional data database http://www.nematodes.org/
PLANMINE Platform for archiving and mining planarian biodiversity http://planmine.mpi-cbg.de/
WORMBASE Database of Caenorhabditis elegans http://www.wormbase.org
WorfDB Worm ORF database which contains predicted proteins from C. elegans http://worfdb.dfci.harvard.edu/

Vertebrate Genome Databases

FANTOM Functional annotation of mouse full-length cDNA clones http://fantom.gsc.riken.jp/
GWIPS-viz Genomes of human beings and vertebrates http://gwips.ucc.ie
Xenbase Human and Vertebrate Genomes http://www.xenbase.org
Mammalian gene collection Identify and sequence cDNA clones of FL or ORF for human, mouse and rat genes
http://mgc.nci.nih.gov/
PlasmID A repository for collection and distribution of plasmid clones for human and vertebrate genomes
http://plasmid.hms.harvard.edu/
Mouse genome database Mouse genome database for integrated data on the genetics, genomics and biology of
the laboratory mouse

http://www.informatics.jax.org

Human Genome Databases

3DSNP Database for comprehensively annotating the regulatory function of human noncoding SNPs by exploring their 3D interactions with genes and genetically associated SNPs mediated by chromatin loops
http://biotech.bmi.ac.cn/3dsnp/
ENCODE at UCSC Encyclopedia of DNA elements an international a consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements
http://genome.ucsc.edu/ENCODE

GeneAnnot Revises and improves the annotation of affymetrix probe sets

 http://genecards.weizmann.ac.il/geneannot/
Locus reference genome sequences Each sequence is a stable genomic DNA sequence for a region of the human
genome http://www.lrg-sequence.org
QTL match maker Database which integrates QTLs of human mouse and rat genomes to annotate their functional genomes http://pmrc.med.mssm.edu:9090/QTL/jsp/qtlhome.jsp
TIARA Total integrated archive of short-read and array (TIARA) accumulates raw-level personal genomic data from whole genome next-generation sequencing (NGS) and comparative genomic hybridization (CGH) arrays
http://tiara.gmi.ac.kr
TRBASE Database that relates tandem repeats to the gene locations and disease genes in the human genome
http://trbase.ex.ac.uk/
UniSTS A comprehensive database of sequence tagged sites (STSs), each of which is defined by a distinct pair of primer sequences designed for use in a PCR reaction http://www.ncbi.nlm.nih.gov/probe
X:MaP Annotation and visualization of genome structure for Affymetrix exon array analysis
http://annmap.picr.man.ac.uk/
EVOLA A database of human genes and their vertebrate orthologs http://jbirc.jbic.or.jp/hinv/evola/
H-InvDB HumanInvitational database is an integrated database of human genes and transcripts
http://www.h-invitational.jp/
HGPD Human gene and Protein database is a unique database that stores information from human gateway entry clones and in vitro expression data related to human proteins http://hupex.hgpd.jp/entrance/index.html
HRPD Human protein reference database that stores the data related to domain architecture, post-translational
modifications, interaction networks and disease http://www.hprd.org/
LIFEdb A database on the localisation, interaction, functional assays and expression of human proteins
http://www.dkfz.de/gpcf/lifedb.php
NetAffx A database of public affymetrix probesets and annotations http://www.affymetrix.com
ORFDB/ ORFeome Invitrogen initiated program intended to provide the open reading frames (ORFs)
of all human proteins http://orf.invitrogen.com/
dbGaP Database of genotypes and phenotypes http://www.ncbi.nlm.nih.gov/gap
MSY breakpoint mapper STSs on human Y chromosome http://breakpointmapper.wi.mit.edu/
Gene cards An automated, integrated database of human genes, genomic maps, proteins and diseases
http://www.genecards.org/

Genomes of Economically Important and Model Plants
 Medicago trunculata database http://www.medicago.org/
Brassica genome http://www.brassicagenome.net/
Coffee genome hub http://coffee-genome.org/
CottonGen http://www.cottongen.org
Maize genetics and genomics database (MaizeGDB) http://www.maizegdb.org/

The Arabidopsis information resource (TAIR) https://www.arabidopsis.org/
Oryza sativa (ssp. japonica) genome http://www.plantgdb.org/OsGDB/
The rice annotation project database https://rapdb.dna.affrc.go.jp/
PoMaMo—potato maps and more http://www.gabipd.org/projects/Pomamo/
Shanghai rapeseed database http://rapeseed.plantsignal.cn/
Genome database for Rosaceae http://www.rosaceae.org
Solanaceae genomics network http://solgenomics.net/
SoyBase http://soybase.org/
SoyKB—soybean knowledge base http://soykb.org
TED—tomato functional genomics database http://ted.bti.cornell.edu/
TIGR maize database http://maize.tigr.org/
TomatEST DB http://biosrv.cab.unina.it/tomatestdb/
TomatEST DB http://biosrv.cab.unina.it/tomatestdb/
PANZEA http://www.panzea.org/
Diatom EST database http://www.biologie.ens.fr/diatomics/
EST/