Virus Databases {#Sec1}
===============

DatabaseDescriptionURLCoVDBCoronavirus genes and genomes<http://covdb.microbiology.hku.hk/>DPV webCentral source of information about viruses, viroids and satellites of plants, fungi, and protozoa<http://www.dpvweb.net/>euHCVdbEuropean hepatitis C virus database<http://euhcvdb.ibcp.fr/>HCV databaseHepatitis C virus database<http://hcv.lanl.gov/>HERVdHuman endogenous retrovirus database<http://herv.img.cas.cz/>HFV databaseHemorrhagic fever virus sequence database<http://hfv.lanl.gov/>HIV drug resistance DBCompilation of mutations in HIV genes that confer resistance to anti-HIV drugs<http://www.hiv.lanl.gov/content/sequence/RESDB/>Influenza research DBInfluenza virus[http://www.fludb.org](http://www.fludb.org/)NCBI viral genomesViral genomes resource<http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html>Papillomavirus epistemeA database of Papillomaviridae family of viruses[http://PaVE.niaid.nih.gov](http://pave.niaid.nih.gov/)phiSITEGene regulation in bacteriophages[http://www.phisite.org](http://www.phisite.org/)Poxvirus .orgPoxvirus genomic sequences and gene annotation<http://www.poxvirus.org/>VBRCViral bioinformatics resource center<http://www.biovirus.org/>ViTamicroRNAs targets of the influenza virus<http://vita.mbc.nctu.edu.tw/>ViralZoneMolecular and epidemiological information on viral genera and families<http://viralzone.expasy.org/>ViralGenomesViral sequence data resource by NCBI<https://www.ncbi.nlm.nih.gov/genome/viruses/>

Archaeal Databases {#Sec2}
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DatabaseDescriptionURLEnsemblA browser for archaeal genomes<https://bacteria.ensembl.org/index.html>EZ cloudEZ cloud for archaea<http://www.ezbiocloud.net/ezgenome>IMGIntegrated microbial genomes and microbiomes<https://img.jgi.doe.gov/>MicrobesOnline resourceA collection of 3707 microbial genomes<http://www.microbesonline.org/>BacDiveThe bacterial diversity metadatabase contains detailed information on more than 20,000 strains of bacteria<https://bacdive.dsmz.de/>WikipediaList of sequenced archaeal genomes<https://en.wikipedia.org/wiki/List_of_sequenced_archaeal_genomes>UCSC archaeal genome browserIntegrated genome browser for archaeal genomes<http://archaea.ucsc.edu/>

Bacterial Databases {#Sec3}
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DatabaseDescriptionURLEnsembl bacteriaA browser for bacterial and archaeal genomes<https://bacteria.ensembl.org/index.html>MBGDDatabase for comparative analysis of completely sequenced microbial genomes<http://mbgd.genome.ad.jp/>Human microbiome projectCharacterisation of microbes in healthy humans<https://hmpdacc.org/>GOLDGenomes online database<https://gold.jgi.doe.gov/>EZ cloudEZ cloud for bacteria<http://www.ezbiocloud.net/ezgenome>IMGIntegrated microbial genomes and microbiomes<https://img.jgi.doe.gov/>MicrobesOnline resourceA collection of 3707 mmicrobial genomes<http://www.microbesonline.org/>BacDiveThe bacterial diversity metadatabase contains detailed information on more than 20,000 strains of bacteria<https://bacdive.dsmz.de/>BIGSdbBacterial isolate genome sequence database<https://bigsdb.readthedocs.io/en/latest/>metaMicrobesOnlineWebsite for browsing and comparing the genomes of 3527 microbial genomes<http://meta.microbesonline.org/>MetaRefA pan-genomic database for comparative and community microbial genomics<https://omictools.com/metaref-tool>MetaBioME databaseMetaBioME 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/>PATRICPathosystems resource integration center<https://www.patricbrc.org/>TBDBTuberculosis database integrates genomic sequences and data for *Mycobacterium* species relevant to drug discovery, vaccines, and biomarkers<http://www.tbdb.org/>EuPathDBEukaryotic pathogen database resources is a collection of individual databases, each focusing on specific pathogens, accessible through a common portal<https://eupathdb.org/>coliBaseA database for *E. coli*, *Salmonella* and *Shigella*<http://xbase.warwick.ac.uk/colibase/>DEGDatabase of essential genes from bacteria and yeast[http://www.essentialgene.org](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>GenoBaseEscherichia coli K-12 in-frame, single-gene knockout mutants<http://ecoli.naist.jp/>HGT-DBHorizantal 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 databaseConsists of information about Pseudomonas genome<http://www.pseudomonas.com/>PAIDBPathogeneticity islands database<http://www.paidb.re.kr/about_paidb.php>

Cell Organelle Databases {#Sec4}
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DatabaseDescriptionURLChloroplast genome databaseChloroplast genome<http://chloroplast.cbio.psu.edu/>OrganelleDBA web-accessible database cataloging proteins localized to a known organelle<http://organelledb.lsi.umich.edu/>Organelle genomesOrganelle genome resource at NCBI[www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html](http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html)Plant organelles databaseImages 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 basePlastid lineage-based conserved gene-pair database<http://lcgbase.big.ac.cn/plastid-LCGbase/>HMPDHuman mitochondrial protein database<http://bioinfo.nist.gov/hmpd/>HmtDBHuman mitochondrial DataBase<http://www.hmtdb.uniba.it/>MamMiBaseDatabase of complete mitochondrial genome sequences of over 100 mammalian species<http://www.mammibase.lncc.br/>MitoCartaMouse and human mitochondrial proteins<http://www.broadinstitute.org/pubs/MitoCarta>MitoDromeAnnotating D. melanogaster nuclear genes encoding mitochondrial proteins and support studies on human diseases related to mitochondrial dysfunctions<http://mitodrome.ba.itb.cnr.it/>MitoPorteomeMitochondrial protein sequences encoded by mitochondrial and nuclear genes<http://www.mitoproteome.org/>OGReDatabase containing information on completely sequenced animal mitochondrial genomes of 473 species<http://ogre.mcmaster.ca/>Arabidopsis mitochondrial protein databaseDatabase comprising of experimentally identified proteins in *Arabidopsis* mitochondrial genome[www.plantenergy.uwa.edu.au/applications/ampdb/index.html](http://www.plantenergy.uwa.edu.au/applications/ampdb/index.html)

In-Vertebrate Genome Databases {#Sec5}
==============================

DatabaseDescriptionURLAphidBaseGenome database of pea aphid (*Acyrthosiphon pisum*)<http://www.aphidbase.com/>AppaDBDatabase of nematode *Pristionchus pacificus*[http://appadb.eb.tuebingen.mpg.de](http://appadb.eb.tuebingen.mpg.de/)BeetleBaseDatabase of the beetle *Tribolium castaneum*[http://www.beetlebase.org](http://www.beetlebase.org/)CeNDR*C. elegans* natural diversity resource[http://www.elegansvariation.org](http://www.elegansvariation.org/)ComparasiteDatabase for comparative studies of transcriptomes of parasites<http://comparasite.hgc.jp/>CuticleDBStructural proteins of arthropod cuticle<http://bioinformatics.biol.uoa.gr/cuticleDB/>FlyBrainDatabase of drosophila nervous system<http://flybrain.neurobio.arizona.edu/>[Helminth.net](http://helminth.net)Parasitic nematode sequencing project[http://www.helminth.net](http://www.helminth.net/)InsectBaseInsect genomes and transcriptomes<http://www.insect-genome.com/>Hymenoptera genomeGenome sequences and annotation for honey bee and the parasitoid wasp *Nasonia vitripennis*[http://HymenopteraGenome.org](http://hymenopteragenome.org/)InsectBaseInsect genomes and transcriptomes<http://www.insect-genome.com/>SilksatDBComprehensive relational database of silkworm microsatellite<http://www.cdfd.org.in/SILKSAT/index.php>SpodoBaseGenomics of the butterfly *Spodoptera frugiperda*<http://bioweb.ensam.inra.fr/spodobase/>VectorBaseInvertebrate vectors of human pathogens[http://www.vectorbase.org](http://www.vectorbase.org/)RNAiDBRNAi phenotypic analysis of *C. elegans* genes<http://www.rnai.org/>NEMBASENematode sequence and functional data database<http://www.nematodes.org/>PLANMINEPlatform for archiving and mining planarian biodiversity<http://planmine.mpi-cbg.de/>WORMBASEDatabase of *Caenorhabditis elegans*[http://www.wormbase.org](http://www.wormbase.org/)WorfDBWorm ORF database which contains predicted proteins from *C. elegans*<http://worfdb.dfci.harvard.edu/>

Vertebrate Genome Databases {#Sec6}
===========================

DatabaseDescriptionURLFANTOMFunctional annotation of mouse full-length cDNA clones<http://fantom.gsc.riken.jp/>GWIPS-vizGenomes of human beings and vertebrates[http://gwips.ucc.ie](http://gwips.ucc.ie/)Xenbase[Human and Vertebrate Genomes](https://www.oxfordjournals.org/nar/database/cat/7)[http://www.xenbase.org](http://www.xenbase.org/)Mammalian gene collectionIdentify and sequence cDNA clones of FL or ORF for human, mouse and rat genes<http://mgc.nci.nih.gov/>PlasmIDA repository for collection and distribution of plasmid clones for human and vertebrate genomes<http://plasmid.hms.harvard.edu/>Mouse genome databaseMouse genome database for integrated data on the genetics, genomics and biology of the laboratory mouse[http://www.informatics.jax.org](http://www.informatics.jax.org/)

Human Genome Databases {#Sec7}
======================

DatabaseDescriptionURL3DSNPDatabase 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 UCSCEncyclopedia 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>GeneAnnotRevises and improves the annotation of affymetrix probe sets<http://genecards.weizmann.ac.il/geneannot/>Locus reference genome sequencesEach sequence is a stable genomic DNA sequence for a region of the human genome[http://www.lrg-sequence.org](http://www.lrg-sequence.org/)QTL match makerDatabase which integrates QTLs of human mouse and rat genomes to annotate their functional genomes<http://pmrc.med.mssm.edu:9090/QTL/jsp/qtlhome.jsp>TIARATotal 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](http://tiara.gmi.ac.kr/)TRBASEDatabase that relates tandem repeats to the gene locations and disease genes in the human genome<http://trbase.ex.ac.uk/>UniSTSA 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:MaPAnnotation and visualization of genome structure for Affymetrix exon array analysis<http://annmap.picr.man.ac.uk/>EVOLAA database of human genes and their vertebrate orthologs<http://jbirc.jbic.or.jp/hinv/evola/>H-InvDBHumanInvitational database is an integrated database of human genes and transcripts<http://www.h-invitational.jp/>HGPDHuman 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>HRPDHuman protein reference database that stores the data related to domain architecture, post-translational modifications, interaction networks and disease<http://www.hprd.org/>LIFEdbA database on the localisation, interaction, functional assays and expression of human proteins<http://www.dkfz.de/gpcf/lifedb.php>NetAffxA database of public affymetrix probesets and annotations<http://www.affymetrix.com>ORFDB/ORFeomeInvitrogen initiated program intended to provide the open reading frames (ORFs) of all human proteins<http://orf.invitrogen.com/>dbGaPDatabase of genotypes and phenotypes<http://www.ncbi.nlm.nih.gov/gap>MSY breakpoint mapperSTSs on human Y chromosome<http://breakpointmapper.wi.mit.edu/>Gene cardsAn automated, integrated database of human genes, genomic maps, proteins and diseases<http://www.genecards.org/>

Plant Genome Databases {#Sec8}
======================

DatabaseDescriptionURLAgBaseA curated, open-source, web-accessible resource for functional analysis of agricultural plant and animal gene products<http://www.agbase.msstate.edu/>autoSNPdbPlant SNP discovery database<http://autosnpdb.appliedbioinformatics.com.au/>BarleyBaseDatabase 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 databaseAn integrated resource for small RNAs such as miRNAs, siRNAs, ta-siRNAs expressed in rice and maize<http://sundarlab.ucdavis.edu/smrnas/>CR-ESTCrop EST database<https://apex.ipk-gatersleben.de/apex/f?p=116:1>EURISCOEuropean catalogue for plant genetic resources<http://eurisco.ecpgr.org/>GABiPDGenome analysis of the plant biological system<http://www.gabipd.org/>GoMapManUnified plant-specific gene ontology[http://www.gomapman.org](http://www.gomapman.org/)GrainGenesMolecular and phenotypic information on grain yielding plants such as wheat, barley, rye, triticale, and oats<http://wheat.pw.usda.gov/>GreeNCGreen 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 databasePlant database resource for integrative and comparative plant genome research<http://mips.gsf.de/proj/plant/jsf/>NIASDatabases for plant genetic resources and plant disease information<http://www.gene.affrc.go.jp/databases_en.php>P-MITEDatabase of plant miniature inverted-repeat transposable elements (MITEs)<http://pmite.hzau.edu.cn/django/mite/>PGDDA plant genome duplication database<http://chibba.agtec.uga.edu/duplication/>PhytozomeA database for green plant genomics<http://www.phytozome.net/>PIECEDatabase of plant intron exon comparison and evolution<https://wheat.pw.usda.gov/piece/>Plant DNA C-values databaseA database that provides a one-stop, user-friendly database where the plant genome sizes can be readily accessed and compared<http://www.kew.org/genomesize/homepage.html>Plant ontology databaseThis 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 databaseA database of snoRNA genes in plant species<http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home>Plant stress-responsive gene catalogStress-responsive gene in various plant species<http://dayhoff.generationcp.org/>Plant GDBA database of plant genomic sequences and ESTs<http://www.plantgdb.org/>Plant PANPlant promoter analysis navigator database[http://PlantPAN2.itps.ncku.edu.tw](http://plantpan2.itps.ncku.edu.tw/)PlantPromA database of plant promoter sequences<http://www.epd.isb-sib.ch/>PlantsP/PlantsTPlantsP and PlantsT are plant-specific curated databases that combine sequence derived information with experimental functional genomics data<http://plantsp.sdsc.edu/>Plant tribesFamilies of protein-coding genes from five sequenced plant species<http://fgp.huck.psu.edu/tribedb/index.pl>PlantTFDBPlant 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](http://planttfdb.cbi.pku.edu.cn/)PLAZAA plant-oriented online resource for comparative, evolutionary and functional genomics<https://bioinformatics.psb.ugent.be/plaza>PMDBaseA database of plant microsatellites and marker development<http://www.sesame-bioinfo.org/PMDBase>TIGR databasePlant transcript assemblies database<http://plantta.tigr.org/>TROPGeneA database comprising of genetic and genomic information about tropical crops such as banana, coconut, cotton, cocoa, etc.<http://tropgenedb.cirad.fr/>ForestTreeA resource that centralizes large-scale<http://foresttree.org/ftdb>DataBaseEST sequencing results from several tree speciesLegumelIPModel legumes integrative database platform<http://plantgrn.noble.org/LegumeIP/>

Genomes of Economically Important and Model Plants {#Sec9}
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DatabaseURL*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](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](http://www.rosaceae.org/)Solanaceae genomics network<http://solgenomics.net/>SoyBase<http://soybase.org/>SoyKB---soybean knowledge base[http://soykb.org](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/>
