Abstract
Genome databases are the locations, which permits storing, sharing, retrieving and comparison of the information related to the genomes of various individuals and organisms. Traditionally the databases were confined to the updated information of certain vital model organisms. Rapid development of technology and high speed internet facilities have created an explosion of databases resulting in the development of specific databases of almost all model organisms and a group of organisms with a common specificity. In the present chapter, details of the databases related to the genomes of viruses, archaea, bacteria, cell organelle, invertebrates, vertebrates, plants, and human beings are provided in a table format which provides an instant information, about different databases and their URLs.
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9.1 Virus Databases
Database | Description | URL |
---|---|---|
CoVDB | Coronavirus genes and genomes | |
DPV web | Central source of information about viruses, viroids and satellites of plants, fungi , and protozoa | |
euHCVdb | European hepatitis C virus database | |
HCV database | Hepatitis C virus database | |
HERVd | Human endogenous retrovirus database | |
HFV database | Hemorrhagic fever virus sequence database | |
HIV drug resistance DB | Compilation of mutations in HIV genes that confer resistance to anti-HIV drugs | |
Influenza research DB | Influenza virus | |
NCBI viral genomes | Viral genomes resource | |
Papillomavirus episteme | A database of Papillomaviridae family of viruses | |
phiSITE | Gene regulation in bacteriophages | |
Poxvirus .org | Poxvirus genomic sequences and gene annotation | |
VBRC | Viral bioinformatics resource center | |
ViTa | microRNAs targets of the influenza virus | |
ViralZone | Molecular and epidemiological information on viral genera and families | |
ViralGenomes | Viral sequence data resource by NCBI |
9.2 Archaeal Databases
Database | Description | URL |
---|---|---|
Ensembl | A browser for archaeal genomes | |
EZ cloud | EZ cloud for archaea | |
IMG | Integrated microbial genomes and microbiomes | |
MicrobesOnline resource | A collection of 3707 microbial genomes | |
BacDive | The bacterial diversity metadatabase contains detailed information on more than 20,000 strains of bacteria | |
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 |
9.3 Bacterial Databases
Database | Description | URL |
---|---|---|
Ensembl bacteria | A browser for bacterial and archaeal genomes | |
MBGD | Database for comparative analysis of completely sequenced microbial genomes | |
Human microbiome project | Characterisation of microbes in healthy humans | |
GOLD | Genomes online database | |
EZ cloud | EZ cloud for bacteria | |
IMG | Integrated microbial genomes and microbiomes | |
MicrobesOnline resource | A collection of 3707 mmicrobial genomes | |
BacDive | The bacterial diversity metadatabase contains detailed information on more than 20,000 strains of bacteria | |
BIGSdb | Bacterial isolate genome sequence database | |
metaMicrobesOnline | Website for browsing and comparing the genomes of 3527 microbial genomes | |
MetaRef | A pan-genomic database for comparative and community microbial genomics | |
MetaBioME database | MetaBioME is a web resource to find novel homologs for known commercially useful enzymes (CUEs) in metagenomic datasets and completed bacterial genomes | |
PATRIC | Pathosystems resource integration center | |
TBDB | Tuberculosis database integrates genomic sequences and data for Mycobacterium species relevant to drug discovery, vaccines, and biomarkers | |
EuPathDB | Eukaryotic pathogen database resources is a collection of individual databases, each focusing on specific pathogens, accessible through a common portal | |
coliBase | A database for E. coli, Salmonella and Shigella | |
DEG | Database of essential genes from bacteria and yeast | |
Essential genes in E.coli | First results of an E. coli gene deletion project | |
GenoBase | Escherichia coli K-12 in-frame, single-gene knockout mutants | |
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 | |
Pseudomonas genome database | Consists of information about Pseudomonas genome | |
PAIDB | Pathogeneticity islands database |
9.4 Cell Organelle Databases
Database | Description | URL |
---|---|---|
Chloroplast genome database | Chloroplast genome | |
OrganelleDB | A web-accessible database cataloging proteins localized to a known organelle | |
Organelle genomes | Organelle genome resource at NCBI | |
Plant organelles database | Images of plant organelles and protocols for plant organelle research | |
PLProt | Arabidopsis thaliana chloroplast protein database | |
Plastid-LCG base | Plastid lineage-based conserved gene-pair database | |
HMPD | Human mitochondrial protein database | |
HmtDB | Human mitochondrial DataBase | |
MamMiBase | Database of complete mitochondrial genome sequences of over 100 mammalian species | |
MitoCarta | Mouse and human mitochondrial proteins | |
MitoDrome | Annotating D. melanogaster nuclear genes encoding mitochondrial proteins and support studies on human diseases related to mitochondrial dysfunctions | |
MitoPorteome | Mitochondrial protein sequences encoded by mitochondrial and nuclear genes | |
OGRe | Database containing information on completely sequenced animal mitochondrial genomes of 473 species | |
Arabidopsis mitochondrial protein database | Database comprising of experimentally identified proteins in Arabidopsis mitochondrial genome |
9.5 In-Vertebrate Genome Databases
Database | Description | URL |
---|---|---|
AphidBase | Genome database of pea aphid (Acyrthosiphon pisum) | |
AppaDB | Database of nematode Pristionchus pacificus | |
BeetleBase | Database of the beetle Tribolium castaneum | |
CeNDR | C. elegans natural diversity resource | |
Comparasite | Database for comparative studies of transcriptomes of parasites | |
CuticleDB | Structural proteins of arthropod cuticle | |
FlyBrain | Database of drosophila nervous system | |
Parasitic nematode sequencing project | ||
InsectBase | Insect genomes and transcriptomes | |
Hymenoptera genome | Genome sequences and annotation for honey bee and the parasitoid wasp Nasonia vitripennis | |
InsectBase | Insect genomes and transcriptomes | |
SilksatDB | Comprehensive relational database of silkworm microsatellite | |
SpodoBase | Genomics of the butterfly Spodoptera frugiperda | |
VectorBase | Invertebrate vectors of human pathogens | |
RNAiDB | RNAi phenotypic analysis of C. elegans genes | |
NEMBASE | Nematode sequence and functional data database | |
PLANMINE | Platform for archiving and mining planarian biodiversity | |
WORMBASE | Database of Caenorhabditis elegans | |
WorfDB | Worm ORF database which contains predicted proteins from C. elegans |
9.6 Vertebrate Genome Databases
Database | Description | URL |
---|---|---|
FANTOM | Functional annotation of mouse full-length cDNA clones | |
GWIPS-viz | Genomes of human beings and vertebrates | |
Xenbase | ||
Mammalian gene collection | Identify and sequence cDNA clones of FL or ORF for human, mouse and rat genes | |
PlasmID | A repository for collection and distribution of plasmid clones for human and vertebrate genomes | |
Mouse genome database | Mouse genome database for integrated data on the genetics, genomics and biology of the laboratory mouse |
9.7 Human Genome Databases
Database | Description | URL |
---|---|---|
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 | |
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 | |
GeneAnnot | Revises and improves the annotation of affymetrix probe sets | |
Locus reference genome sequences | Each sequence is a stable genomic DNA sequence for a region of the human genome | |
QTL match maker | Database which integrates QTLs of human mouse and rat genomes to annotate their functional genomes | |
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 | |
TRBASE | Database that relates tandem repeats to the gene locations and disease genes in the human genome | |
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 | |
X:MaP | Annotation and visualization of genome structure for Affymetrix exon array analysis | |
EVOLA | A database of human genes and their vertebrate orthologs | |
H-InvDB | HumanInvitational database is an integrated database of human genes and transcripts | |
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 | |
HRPD | Human protein reference database that stores the data related to domain architecture, post-translational modifications, interaction networks and disease | |
LIFEdb | A database on the localisation, interaction, functional assays and expression of human proteins | |
NetAffx | A database of public affymetrix probesets and annotations | |
ORFDB/ORFeome | Invitrogen initiated program intended to provide the open reading frames (ORFs) of all human proteins | |
dbGaP | Database of genotypes and phenotypes | |
MSY breakpoint mapper | STSs on human Y chromosome | |
Gene cards | An automated, integrated database of human genes, genomic maps, proteins and diseases |
9.8 Plant Genome Databases
Database | Description | URL |
---|---|---|
AgBase | A curated, open-source, web-accessible resource for functional analysis of agricultural plant and animal gene products | |
autoSNPdb | Plant SNP discovery database | |
BarleyBase | Database for barley microarrays holds the data for over 1000 hybridizations from the affymetrix Barley1 GeneChip and genome arrays | |
Cereal small RNA database | An integrated resource for small RNAs such as miRNAs, siRNAs, ta-siRNAs expressed in rice and maize | |
CR-EST | Crop EST database | |
EURISCO | European catalogue for plant genetic resources | |
GABiPD | Genome analysis of the plant biological system | |
GoMapMan | Unified plant-specific gene ontology | |
GrainGenes | Molecular and phenotypic information on grain yielding plants such as wheat, barley, rye, triticale, and oats | |
GreeNC | Green non-coding database (GreeNC) is a repository of long non-coding RNAs annotated in 37 plant species and six algae | |
MIPS plants database | Plant database resource for integrative and comparative plant genome research | |
NIAS | Databases for plant genetic resources and plant disease information | |
P-MITE | Database of plant miniature inverted-repeat transposable elements (MITEs) | |
PGDD | A plant genome duplication database | |
Phytozome | A database for green plant genomics | |
PIECE | Database of plant intron exon comparison and evolution | |
Plant DNA C-values database | A database that provides a one-stop, user-friendly database where the plant genome sizes can be readily accessed and compared | |
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 | |
Plant SnoRNA database | A database of snoRNA genes in plant species | |
Plant stress-responsive gene catalog | Stress-responsive gene in various plant species | |
Plant GDB | A database of plant genomic sequences and ESTs | |
Plant PAN | Plant promoter analysis navigator database | |
PlantProm | A database of plant promoter sequences | |
PlantsP/PlantsT | PlantsP and PlantsT are plant-specific curated databases that combine sequence derived information with experimental functional genomics data | |
Plant tribes | Families of protein-coding genes from five sequenced plant species | |
PlantTFDB | Plant transcription factor database provides a comprehensive, high-quality resource of plant transcription factors, regulatory elements and interactions between them | |
PLAZA | A plant-oriented online resource for comparative, evolutionary and functional genomics | |
PMDBase | A database of plant microsatellites and marker development | |
TIGR database | Plant transcript assemblies database | |
TROPGene | A database comprising of genetic and genomic information about tropical crops such as banana, coconut, cotton, cocoa, etc. | |
ForestTree | A resource that centralizes large-scale | |
DataBase | EST sequencing results from several tree species | |
LegumelIP | Model legumes integrative database platform |
9.9 Genomes of Economically Important and Model Plants
Database | URL |
---|---|
Medicago trunculata database | |
Brassica genome | |
Coffee genome hub | |
CottonGen | |
Maize genetics and genomics database (MaizeGDB) | |
The Arabidopsis information resource (TAIR) | |
Oryza sativa (ssp. japonica) genome | |
The rice annotation project database | |
PoMaMo—potato maps and more | |
Shanghai rapeseed database | |
Genome database for Rosaceae | |
Solanaceae genomics network | |
SoyBase | |
SoyKB—soybean knowledge base | |
TED—tomato functional genomics database | |
TIGR maize database | |
TomatEST DB | |
TomatEST DB | |
PANZEA | |
Diatom EST database |
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Chaitanya, K.V. (2019). Important Databases Related to Genomes. In: Genome and Genomics. Springer, Singapore. https://doi.org/10.1007/978-981-15-0702-1_9
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DOI: https://doi.org/10.1007/978-981-15-0702-1_9
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