9.1 Virus Databases

Database

Description

URL

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/

9.2 Archaeal Databases

Database

Description

URL

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/

9.3 Bacterial Databases

Database

Description

URL

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

9.4 Cell Organelle Databases

Database

Description

URL

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-pair database

http://lcgbase.big.ac.cn/plastid-LCGbase/

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

9.5 In-Vertebrate Genome Databases

Database

Description

URL

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/

9.6 Vertebrate Genome Databases

Database

Description

URL

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

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

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/

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

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/smrnas/

CR-EST

Crop EST database

https://apex.ipk-gatersleben.de/apex/f?p=116:1

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-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-friendly 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-bin/plant_snorna/home

Plant stress-responsive 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/

9.9 Genomes of Economically Important and Model Plants

Database

URL

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/