Genome and Organism Specific List of 111 Databases

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.
Genome and Organism Specific Databases
Genome and Organism Specific Databases

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:

List of 15 Virus Databases

DatabaseDescriptionURL
CoVDBGene and genomes of coronavirushttp://covdb.microbiology.hku.hk/
DPV webIt is the source of information for viruses, viroids, and satellites of plants, fungus, and protozoahttp://www.dpvweb.net/
euHCVdbIt is the database for European hepatitis Chttp://euhcvdb.ibcp.fr/
HCV databaseDatabase for Hepatitis Chttp://hcv.lanl.gov/
HERVdDatabase for human endogenous retrovirushttp://herv.img.cas.cz/
HFV databaseDatabase for hemorrhagic fever virus sequencehttp://hfv.lanl.gov/
HIV drug resistance DBDatabase for the compilation of mutations in HIV geneshttp://www.hiv.lanl.gov/content/sequence/RESDB/
Influenza research DBDatabase for Influenza virushttp://www.fludb.org/
NCBI viral genomesDatabase for viral genome researchhttp://www.ncbi.nlm.nih.gov/
genomes/VIRUSES/viruses.html
Papillomavirus epistemeDatabase for  Papillomaviridae family of viruseshttp://pave.niaid.nih.gov/
phiSITEDatabase for gene regulation in bacteriophageshttp://www.phisite.org/
Poxvirus .orgDatabase for poxvirus genome and gene annotationhttp://www.poxvirus.org/
VBRCDatabase for the viral informatics research centerhttp://www.biovirus.org/
ViTaDatabase for the microRNA of the influenza virushttp://vita.mbc.nctu.edu.tw/
ViralZoneDatabase for molecular and epidemiological information on viral generahttps://www.ncbi.nlm.nih.gov/genome/viruses/

List of 7 Archaeal Databases

DatabaseDetailsURL
EnsemblDatabase for archaeal genomeshttps://bacteria.ensembl.org/index.html
EZ cloudDatabase cloud for archaeahttp://www.ezbiocloud.net/ezgenome
IMGDatabase for integrated microbial genomes and microbeshttps://img.jgi.doe.gov/
MicrobesOnline resourceDatabase for the 3707 microbial genomeshttp://www.microbesonline.org/
BacDiveDatabase for bacterial diversityhttps://bacdive.dsmz.de/
WikipediaDatabase for sequenced archaeal genomeshttps://en.wikipedia.org/wiki/
List_of_sequenced_archaeal_genomes
UCSC archaeal genome browserDatabase for integrated genome browser of archaeal genomeshttp://archaea.ucsc.edu/

List of 19 Bacterial Databases

Database Details URL
Ensembl bacteriaDatabase for bacterial and archaeal genomehttps://bacteria.ensembl.org/index.html
MBGDDatabase for analysis of completely sequenced microbial genomeshttp://mbgd.genome.ad.jp/
Human microbiome projectDatabase for the characterization of the microbiomes in healthy humanshttps://hmpdacc.org/
GOLDDatabase for online genomeshttps://gold.jgi.doe.gov/
EZ cloudDatabase cloud for bacteriahttp://www.ezbiocloud.net/ezgenome
IMGDatabase for integrated microbial genome and microbiomeshttps://img.jgi.doe.gov/
Microbes Online resourceDatabase that has the collection of 3707 microbial genomeshttp://www.microbesonline.org/
BacDiveDatabase for bacterial diversity https://bacdive.dsmz.de/
BIGSdbDatabase for bacterial isolates genomeshttps://bigsdb.readthedocs.io/en/latest/
metaMicrobesOnlineDatabase that collects 3527 microbial genomes where one can browse and compare the genome of interesthttp://meta.microbesonline.org/
MetaRefDatabase for comparative and community microbial genomeshttps://omictools.com/metaref-tool
MetaBioME databaseDatabase for metagenomics and completed bacterial genomeshttps://metasystems.riken.jp/metabiome/
PATRICDatabase for pathosystems resource integration centerhttps://www.patricbrc.org/
TBDBDatabase for tuberculosis and mycobacterium species relevant to drug discovery, vaccines, and biomarkershttp://www.tbdb.org/
EuPathDBDatabase for eukaryotic pathogenshttps://eupathdb.org/
coliBaseDatabase for E.coli, salmonella, and shigellahttp://xbase.warwick.ac.uk/colibase/
DEGDatabase for bacteria and yeastshttp://www.essentialgene.org/
GenoBaseDatabase for Escherichia Coli K-12 and single-gene knockout mutantshttp://ecoli.naist.jp/
HGT-DBDatabase for horizontal gene transferhttp://genomes.urv.es/HGT-DB/

List of 14 Cell Organelle Databases

DatabaseDetailsURL
Chloroplast genome databaseDatabase for chloroplast genomehttp://chloroplast.cbio.psu.edu/
OrganelleDBDatabase for proteins localized to known organelleshttp://organelledb.lsi.umich.edu/
Organelle genomesDatabase for organelle genomehttp://www.ncbi.nlm.nih.gov/
genomes/ORGANELLES/organelles.html
Plant organelles databaseDatabase for the images of the plant organelles and protocol for plant organelles researchhttp://podb.nibb.ac.jp/Organellome/
PLProtDatabase for Arabidopsis thaliana chloroplast proteinhttp://www.plprot.ethz.ch/
Plastid-LCG baseDatabase for plastid lineage-based conserved gene pairhttp://lcgbase.big.ac.cn/plastid-LCGbase/
HMPDDatabase for human mitochondrial proteinshttp://bioinfo.nist.gov/hmpd/
HmtDBDatabase for human mitochondrialhttp://www.hmtdb.uniba.it/
MamMiBaseDatabase for complete mitochondrial genomehttp://www.mammibase.lncc.br/
MitoCartaDatabase for mouse and human mitochondrial proteinshttp://www.broadinstitute.org/
pubs/MitoCarta
MitoDromeDatabase for Annotating D. melanogaster nuclear genes encoding mitochondrial proteins http://mitodrome.ba.itb.cnr.it/
MitoPorteomeDatabase for mitochondrial protein sequences encoded by mitochondrial and nuclear geneshttp://www.mitoproteome.org/
OGReDatabase of the completely sequenced animal mitochondrial genome of 473 specieshttp://ogre.mcmaster.ca/
Arabidopsis mitochondrial protein databaseA database comprising experimentally identified proteins in Arabidopsis mitochondrial genomehttp://www.plantenergy.uwa.edu.au/
applications/ampdb/index.html

List of 18 Invertebrate Genome Databases

Database Details URL
AphidBaseDatabase for pea aphids genomehttp://www.aphidbase.com/
AppaDBDatabase for nematode Pristionchus pacificushttp://appadb.eb.tuebingen.mpg.de/
BeetleBaseDatabase for beetle Tribolium castaneumhttp://www.beetlebase.org/
CeNDRDatabase for c. eleganshttp://www.elegansvariation.org/
ComparasiteDatabase for transcriptomes of parasiteshttp://comparasite.hgc.jp/
CuticleDBDatabase for Structural proteins of arthropod cuticlehttp://bioinformatics.biol.uoa.gr/cuticleDB/
FlyBrainDatabase for drosophila nervous systemhttp://flybrain.neurobio.arizona.edu/
InsectBaseDatabase for insect genome and transcriptomeshttp://www.insect-genome.com/
Hymenoptera genomeDatabase for honey bee and the parasitoid wasp Nasonia vitripennishttp://hymenopteragenome.org/
InsectBaseDatabase for insect genomes and transcriptomeshttp://www.insect-genome.com/
SilksatDBDatabase for silkworm microsatellitehttp://www.cdfd.org.in/SILKSAT/index.php
SpodoBaseDatabase for Genomics of the butterfly Spodoptera frugiperdahttp://bioweb.ensam.inra.fr/spodobase/
VectorBaseDatabase for an invertebrate vector of the human pathogenhttp://www.vectorbase.org/
RNAiDBDatabase for RNAi phenotypic analysis of C. elegans geneshttp://www.rnai.org/
NEMBASEDatabase for nematode sequences and functional databasehttp://www.nematodes.org/
PLANMINEDatabase for archiving and mining planarian biodiversity http://planmine.mpi-cbg.de/
WORMBASEDatabase for Caenorhabditis eleganshttp://www.wormbase.org/
WorfDBDatabase for predicted proteins from C. elegans http://worfdb.dfci.harvard.edu/

List of 6 Vertebrate Genome Databases

Database Details URL
FANTOMDatabase for functional annotation of mouse full-length cDNA cloneshttp://fantom.gsc.riken.jp/
GWIPS-vizDatabase for genomes of human beings and vertebrateshttp://gwips.ucc.ie/
XenbaseDatabase for human and vertebrate genomehttp://www.xenbase.org/
Mammalian gene collectionDatabase for mouse and rat geneshttp://mgc.nci.nih.gov/
PlasmIDDatabase for the collection and distribution of plasmid clones of human and vertebrate genomeshttp://plasmid.hms.harvard.edu/
Mouse genome databaseDatabase for integrated data on the genetics, genomics, and biology of the laboratory mousehttp://www.informatics.jax.org/

List of 19 Human Genome Databases

Database DetailsURL
3DSNPDatabase for the regulatory function of human noncoding SNPshttp://biotech.bmi.ac.cn/3dsnp/
ENCODE at UCSCDatabase for DNA elementshttp://genome.ucsc.edu/ENCODE
GeneAnnotDatabase for annotation of Affymetrix probe setshttp://genecards.weizmann.ac.il/geneannot/
Locus reference genome sequencesDatabase for a stable sequence of the human genomehttp://www.lrg-sequence.org/
QTL match makerDatabase for human, mouse, and rats genomes http://pmrc.med.mssm.edu:9090/QTL/jsp/qtlhome.jsp
TIARADatabase for raw-level personal genomic data from NGS and CGH arrayhttp://tiara.gmi.ac.kr/
TRBASEDatabase for tandem repeats and diseases gene in the human genomehttp://trbase.ex.ac.uk/
UniSTSDatabase for sequence tagged siteshttp://www.ncbi.nlm.nih.gov/probe
X:MaPDatabase for visualization of the structure of exonhttp://annmap.picr.man.ac.uk/
EVOLADatabase for human genes and orthologs for vertebrateshttp://jbirc.jbic.or.jp/hinv/evola/
H-InvDBDatabase for human genes and transcriptshttp://www.h-invitational.jp/
HGPDDatabase for human genes and in vitro expression related to human proteinshttp://hupex.hgpd.jp/entrance/index.html
HRPDDatabase for human reference protein, post-translation modification, interaction network, and diseaseshttp://www.hprd.org/
LIFEdbDatabase for human proteins interaction, function, interaction, and localizationhttp://www.dkfz.de/gpcf/lifedb.php
NetAffxDatabase for probesets and annotationshttp://www.affymetrix.com/
ORFDB/ORFeomeDatabase for open reading frames of human proteinshttp://orf.invitrogen.com/
dbGaPDatabase for all of the genotypes and phenotypeshttp://www.ncbi.nlm.nih.gov/gap
MSY breakpoint mapperDatabase for human Y chromosomehttp://breakpointmapper.wi.mit.edu/
Gene cardsDatabase for the human genome, gene map, proteins, and diseaseshttp://www.genecards.org/

List of 13 Plant Genome Databases

Database Details URL
AgBaseDatabase for agricultural plants and animal gene productshttp://www.agbase.msstate.edu/
autoSNPdbDatabase for plant SNPshttp://autosnpdb.appliedbioinformatics.com.au/
BarleyBaseDatabase for barley microarrayhttp://www.barleybase.org/
Cereal small RNA databaseDatabase for miRNAs, siRNAs, and ta-siRNAs in rice and maizehttp://sundarlab.ucdavis.edu/smrnas/
CR-ESTDatabase for crop ESThttps://apex.ipk-gatersleben.de/apex/f?p=116:1
EURISCODatabase for plant genetic resourceshttp://eurisco.ecpgr.org/
GABiPDDatabase for plant genome biological systemhttp://www.gabipd.org/
GoMapManDatabase for plant-specific genehttp://www.gomapman.org/
GrainGenesDatabase for morphological and phenotypic characteristics of wheat, barley, and oatshttp://wheat.pw.usda.gov/
GreeNCDatabase for long-non coding RNAshttp://greenc.sciencedesigners.com/wiki/Main_Page
MIPS plants databaseDatabase for plant genome researchhttp://mips.gsf.de/proj/plant/jsf/
NIASDatabase for plant genetics and diseases http://www.gene.affrc.go.jp/databases_en.php
P-MITEDatabase for transposable elements of plantshttp://pmite.hzau.edu.cn/django/mite/

References

  1. https://www.genome.gov/10001837/model-organism-databases
  2. https://guides.library.stonybrook.edu/c.php?g=35530&p=1138742
  3. https://link.springer.com/chapter/10.1007/978-981-15-0702-1_9
  4. https://www.researchgate.net/publication/227990866_Genome_Databases
  5. https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/Databases/databases_scope.html
  6. https://link.springer.com/chapter/10.1007/978-981-15-0702-1_9
  7. https://www.nature.com/scitable/topicpage/genomic-data-resources-challenges-and-promises-743721/
  8. https://www.ncbi.nlm.nih.gov/genome/viruses/
  9. https://www.viprbrc.org/
  10. https://academic.oup.com/bioinformatics/article/16/5/484/192501
  11. https://www.genome.jp/virushostdb/
  12. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-595
  13. https://www.ncbi.nlm.nih.gov/genome/microbes/
  14. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165460/
  15. https://www.nature.com/articles/s41564-021-00918-8
  16. https://www.hilarispublisher.com/abstract/archaeprofile-a-database-of-archaea-and-their-origins-of-replication-35356.html
  17. https://academic.oup.com/nar/article/26/1/94/2379498
  18. https://www.hsls.pitt.edu/obrc/index.php?page=human_genome
  19. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308780/
  20. https://plantgarden.jp/en/index

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