Genome databases are the locations where the updated information related to organisms and species is uploaded and stored, and sharing of the information is done. It is also the platform for retrieving and comparison of the information related to the genome of various individuals and organisms. The rapid development of technology and the internet has led to the development of specific databases of almost all organisms and a group of organisms with a common specificity.
- It is the repository of DNA sequences from many different species of plants and animals and helps to interpret the related data by comparison of the sequences from different species.
- Different technologies are used by Molecular Biologists and geneticists for the generation of sequenced data.
There are various databases related to the genome of viruses, archaea, bacteria, cell organelle, invertebrates, vertebrates, plants, and human beings. The details about the database are as follows:
Table of Contents
List of 15 Virus Databases
| Database | Description | URL |
| CoVDB | Gene and genomes of coronavirus | http://covdb.microbiology.hku.hk/ |
| DPV web | It is the source of information for viruses, viroids, and satellites of plants, fungus, and protozoa | http://www.dpvweb.net/ |
| euHCVdb | It is the database for European hepatitis C | http://euhcvdb.ibcp.fr/ |
| HCV database | Database for Hepatitis C | http://hcv.lanl.gov/ |
| HERVd | Database for human endogenous retrovirus | http://herv.img.cas.cz/ |
| HFV database | Database for hemorrhagic fever virus sequence | http://hfv.lanl.gov/ |
| HIV drug resistance DB | Database for the compilation of mutations in HIV genes | http://www.hiv.lanl.gov/content/sequence/RESDB/ |
| Influenza research DB | Database for Influenza virus | http://www.fludb.org/ |
| NCBI viral genomes | Database for viral genome research | http://www.ncbi.nlm.nih.gov/ genomes/VIRUSES/viruses.html |
| Papillomavirus episteme | Database for Papillomaviridae family of viruses | http://pave.niaid.nih.gov/ |
| phiSITE | Database for gene regulation in bacteriophages | http://www.phisite.org/ |
| Poxvirus .org | Database for poxvirus genome and gene annotation | http://www.poxvirus.org/ |
| VBRC | Database for the viral informatics research center | http://www.biovirus.org/ |
| ViTa | Database for the microRNA of the influenza virus | http://vita.mbc.nctu.edu.tw/ |
| ViralZone | Database for molecular and epidemiological information on viral genera | https://www.ncbi.nlm.nih.gov/genome/viruses/ |
List of 7 Archaeal Databases
| Database | Details | URL |
| Ensembl | Database for archaeal genomes | https://bacteria.ensembl.org/index.html |
| EZ cloud | Database cloud for archaea | http://www.ezbiocloud.net/ezgenome |
| IMG | Database for integrated microbial genomes and microbes | https://img.jgi.doe.gov/ |
| MicrobesOnline resource | Database for the 3707 microbial genomes | http://www.microbesonline.org/ |
| BacDive | Database for bacterial diversity | https://bacdive.dsmz.de/ |
| Wikipedia | Database for sequenced archaeal genomes | https://en.wikipedia.org/wiki/ List_of_sequenced_archaeal_genomes |
| UCSC archaeal genome browser | Database for integrated genome browser of archaeal genomes | http://archaea.ucsc.edu/ |
List of 19 Bacterial Databases
| Database | Details | URL |
| Ensembl bacteria | Database for bacterial and archaeal genome | https://bacteria.ensembl.org/index.html |
| MBGD | Database for analysis of completely sequenced microbial genomes | http://mbgd.genome.ad.jp/ |
| Human microbiome project | Database for the characterization of the microbiomes in healthy humans | https://hmpdacc.org/ |
| GOLD | Database for online genomes | https://gold.jgi.doe.gov/ |
| EZ cloud | Database cloud for bacteria | http://www.ezbiocloud.net/ezgenome |
| IMG | Database for integrated microbial genome and microbiomes | https://img.jgi.doe.gov/ |
| Microbes Online resource | Database that has the collection of 3707 microbial genomes | http://www.microbesonline.org/ |
| BacDive | Database for bacterial diversity | https://bacdive.dsmz.de/ |
| BIGSdb | Database for bacterial isolates genomes | https://bigsdb.readthedocs.io/en/latest/ |
| metaMicrobesOnline | Database that collects 3527 microbial genomes where one can browse and compare the genome of interest | http://meta.microbesonline.org/ |
| MetaRef | Database for comparative and community microbial genomes | https://omictools.com/metaref-tool |
| MetaBioME database | Database for metagenomics and completed bacterial genomes | https://metasystems.riken.jp/metabiome/ |
| PATRIC | Database for pathosystems resource integration center | https://www.patricbrc.org/ |
| TBDB | Database for tuberculosis and mycobacterium species relevant to drug discovery, vaccines, and biomarkers | http://www.tbdb.org/ |
| EuPathDB | Database for eukaryotic pathogens | https://eupathdb.org/ |
| coliBase | Database for E.coli, salmonella, and shigella | http://xbase.warwick.ac.uk/colibase/ |
| DEG | Database for bacteria and yeasts | http://www.essentialgene.org/ |
| GenoBase | Database for Escherichia Coli K-12 and single-gene knockout mutants | http://ecoli.naist.jp/ |
| HGT-DB | Database for horizontal gene transfer | http://genomes.urv.es/HGT-DB/ |
List of 14 Cell Organelle Databases
| Database | Details | URL |
| Chloroplast genome database | Database for chloroplast genome | http://chloroplast.cbio.psu.edu/ |
| OrganelleDB | Database for proteins localized to known organelles | http://organelledb.lsi.umich.edu/ |
| Organelle genomes | Database for organelle genome | http://www.ncbi.nlm.nih.gov/ genomes/ORGANELLES/organelles.html |
| Plant organelles database | Database for the images of the plant organelles and protocol for plant organelles research | http://podb.nibb.ac.jp/Organellome/ |
| PLProt | Database for Arabidopsis thaliana chloroplast protein | http://www.plprot.ethz.ch/ |
| Plastid-LCG base | Database for plastid lineage-based conserved gene pair | http://lcgbase.big.ac.cn/plastid-LCGbase/ |
| HMPD | Database for human mitochondrial proteins | http://bioinfo.nist.gov/hmpd/ |
| HmtDB | Database for human mitochondrial | http://www.hmtdb.uniba.it/ |
| MamMiBase | Database for complete mitochondrial genome | http://www.mammibase.lncc.br/ |
| MitoCarta | Database for mouse and human mitochondrial proteins | http://www.broadinstitute.org/ pubs/MitoCarta |
| MitoDrome | Database for Annotating D. melanogaster nuclear genes encoding mitochondrial proteins | http://mitodrome.ba.itb.cnr.it/ |
| MitoPorteome | Database for mitochondrial protein sequences encoded by mitochondrial and nuclear genes | http://www.mitoproteome.org/ |
| OGRe | Database of the completely sequenced animal mitochondrial genome of 473 species | http://ogre.mcmaster.ca/ |
| Arabidopsis mitochondrial protein database | A database comprising experimentally identified proteins in Arabidopsis mitochondrial genome | http://www.plantenergy.uwa.edu.au/ applications/ampdb/index.html |
List of 18 Invertebrate Genome Databases
| Database | Details | URL |
| AphidBase | Database for pea aphids genome | http://www.aphidbase.com/ |
| AppaDB | Database for nematode Pristionchus pacificus | http://appadb.eb.tuebingen.mpg.de/ |
| BeetleBase | Database for beetle Tribolium castaneum | http://www.beetlebase.org/ |
| CeNDR | Database for c. elegans | http://www.elegansvariation.org/ |
| Comparasite | Database for transcriptomes of parasites | http://comparasite.hgc.jp/ |
| CuticleDB | Database for Structural proteins of arthropod cuticle | http://bioinformatics.biol.uoa.gr/cuticleDB/ |
| FlyBrain | Database for drosophila nervous system | http://flybrain.neurobio.arizona.edu/ |
| InsectBase | Database for insect genome and transcriptomes | http://www.insect-genome.com/ |
| Hymenoptera genome | Database for honey bee and the parasitoid wasp Nasonia vitripennis | http://hymenopteragenome.org/ |
| InsectBase | Database for insect genomes and transcriptomes | http://www.insect-genome.com/ |
| SilksatDB | Database for silkworm microsatellite | http://www.cdfd.org.in/SILKSAT/index.php |
| SpodoBase | Database for Genomics of the butterfly Spodoptera frugiperda | http://bioweb.ensam.inra.fr/spodobase/ |
| VectorBase | Database for an invertebrate vector of the human pathogen | http://www.vectorbase.org/ |
| RNAiDB | Database for RNAi phenotypic analysis of C. elegans genes | http://www.rnai.org/ |
| NEMBASE | Database for nematode sequences and functional database | http://www.nematodes.org/ |
| PLANMINE | Database for archiving and mining planarian biodiversity | http://planmine.mpi-cbg.de/ |
| WORMBASE | Database for Caenorhabditis elegans | http://www.wormbase.org/ |
| WorfDB | Database for predicted proteins from C. elegans | http://worfdb.dfci.harvard.edu/ |
List of 6 Vertebrate Genome Databases
| Database | Details | URL |
| FANTOM | Database for functional annotation of mouse full-length cDNA clones | http://fantom.gsc.riken.jp/ |
| GWIPS-viz | Database for genomes of human beings and vertebrates | http://gwips.ucc.ie/ |
| Xenbase | Database for human and vertebrate genome | http://www.xenbase.org/ |
| Mammalian gene collection | Database for mouse and rat genes | http://mgc.nci.nih.gov/ |
| PlasmID | Database for the collection and distribution of plasmid clones of human and vertebrate genomes | http://plasmid.hms.harvard.edu/ |
| Mouse genome database | Database for integrated data on the genetics, genomics, and biology of the laboratory mouse | http://www.informatics.jax.org/ |
List of 19 Human Genome Databases
| Database | Details | URL |
| 3DSNP | Database for the regulatory function of human noncoding SNPs | http://biotech.bmi.ac.cn/3dsnp/ |
| ENCODE at UCSC | Database for DNA elements | http://genome.ucsc.edu/ENCODE |
| GeneAnnot | Database for annotation of Affymetrix probe sets | http://genecards.weizmann.ac.il/geneannot/ |
| Locus reference genome sequences | Database for a stable sequence of the human genome | http://www.lrg-sequence.org/ |
| QTL match maker | Database for human, mouse, and rats genomes | http://pmrc.med.mssm.edu:9090/QTL/jsp/qtlhome.jsp |
| TIARA | Database for raw-level personal genomic data from NGS and CGH array | http://tiara.gmi.ac.kr/ |
| TRBASE | Database for tandem repeats and diseases gene in the human genome | http://trbase.ex.ac.uk/ |
| UniSTS | Database for sequence tagged sites | http://www.ncbi.nlm.nih.gov/probe |
| X:MaP | Database for visualization of the structure of exon | http://annmap.picr.man.ac.uk/ |
| EVOLA | Database for human genes and orthologs for vertebrates | http://jbirc.jbic.or.jp/hinv/evola/ |
| H-InvDB | Database for human genes and transcripts | http://www.h-invitational.jp/ |
| HGPD | Database for human genes and in vitro expression related to human proteins | http://hupex.hgpd.jp/entrance/index.html |
| HRPD | Database for human reference protein, post-translation modification, interaction network, and diseases | http://www.hprd.org/ |
| LIFEdb | Database for human proteins interaction, function, interaction, and localization | http://www.dkfz.de/gpcf/lifedb.php |
| NetAffx | Database for probesets and annotations | http://www.affymetrix.com/ |
| ORFDB/ORFeome | Database for open reading frames of human proteins | http://orf.invitrogen.com/ |
| dbGaP | Database for all of the genotypes and phenotypes | http://www.ncbi.nlm.nih.gov/gap |
| MSY breakpoint mapper | Database for human Y chromosome | http://breakpointmapper.wi.mit.edu/ |
| Gene cards | Database for the human genome, gene map, proteins, and diseases | http://www.genecards.org/ |
List of 13 Plant Genome Databases
| Database | Details | URL |
| AgBase | Database for agricultural plants and animal gene products | http://www.agbase.msstate.edu/ |
| autoSNPdb | Database for plant SNPs | http://autosnpdb.appliedbioinformatics.com.au/ |
| BarleyBase | Database for barley microarray | http://www.barleybase.org/ |
| Cereal small RNA database | Database for miRNAs, siRNAs, and ta-siRNAs in rice and maize | http://sundarlab.ucdavis.edu/smrnas/ |
| CR-EST | Database for crop EST | https://apex.ipk-gatersleben.de/apex/f?p=116:1 |
| EURISCO | Database for plant genetic resources | http://eurisco.ecpgr.org/ |
| GABiPD | Database for plant genome biological system | http://www.gabipd.org/ |
| GoMapMan | Database for plant-specific gene | http://www.gomapman.org/ |
| GrainGenes | Database for morphological and phenotypic characteristics of wheat, barley, and oats | http://wheat.pw.usda.gov/ |
| GreeNC | Database for long-non coding RNAs | http://greenc.sciencedesigners.com/wiki/Main_Page |
| MIPS plants database | Database for plant genome research | http://mips.gsf.de/proj/plant/jsf/ |
| NIAS | Database for plant genetics and diseases | http://www.gene.affrc.go.jp/databases_en.php |
| P-MITE | Database for transposable elements of plants | http://pmite.hzau.edu.cn/django/mite/ |
References
- https://www.genome.gov/10001837/model-organism-databases
- https://guides.library.stonybrook.edu/c.php?g=35530&p=1138742
- https://link.springer.com/chapter/10.1007/978-981-15-0702-1_9
- https://www.researchgate.net/publication/227990866_Genome_Databases
- https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/Databases/databases_scope.html
- https://link.springer.com/chapter/10.1007/978-981-15-0702-1_9
- https://www.nature.com/scitable/topicpage/genomic-data-resources-challenges-and-promises-743721/
- https://www.ncbi.nlm.nih.gov/genome/viruses/
- https://www.viprbrc.org/
- https://academic.oup.com/bioinformatics/article/16/5/484/192501
- https://www.genome.jp/virushostdb/
- https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-595
- https://www.ncbi.nlm.nih.gov/genome/microbes/
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165460/
- https://www.nature.com/articles/s41564-021-00918-8
- https://www.hilarispublisher.com/abstract/archaeprofile-a-database-of-archaea-and-their-origins-of-replication-35356.html
- https://academic.oup.com/nar/article/26/1/94/2379498
- https://www.hsls.pitt.edu/obrc/index.php?page=human_genome
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308780/
- https://plantgarden.jp/en/index