NAR DATABASES

Nucleotide sequence databases.

•International Nucleotide Sequence Database Collaboration
•Coding and non-coding DNA
•Gene structure, introns and exons, splice sites
•Transcriptional regulator sites and transcription factors

RNA sequence databases.

•16S and 23S Ribosomal RNA Mutation Database
•3D rRNA modification maps
•dbRES
•CircNet

Protein sequence databases.

•General sequence databases
•Protein properties
•Protein localization and targeting
•Protein sequence motifs and active sites
•Protein domain databases; protein classification
•Databases of individual protein families

Structure databases.

•BARD
•Small molecules
•Carbohydrates
•Nucleic acid structure
•Protein structure

Genomics databases.

•The Gene Indices
•Genome annotation terms, ontologies and nomenclature
•Taxonomy and identification
•General genomics databases
•Viral genome databases
•Prokaryotic genome databases
•Unicellular eukaryotes genome databases
•Fungal genome databases
•Invertebrate genome databases

Metabolic and Signalling Pathways.

•ChemProt
•Prokaryotic genome databases
•Enzymes and enzyme nomenclature
•Metabolic pathways
•Protein-protein interactions
•Signalling pathways

Human and other vertebrate Genomes.

•Model organisms, comparative genomics
•Human genome databases, maps and viewers
•Human ORFs

Human Genes and Diseases.

•CancerResource
•DriverDBv2
•Protein Mutant Database
•General human genetics databases
•General polymorphism databases
•Cancer gene databases

Microarray Data and other Gene Expression databases.

•CAGE
•CATMA - Complete Arabidopsis Transcriptome MicroArray
•CEBS
•CGED - Cancer Gene Expression Database
•Gene Expression Barcode

Proteomics Resources

•2D-PAGE
•AAindex
•Open Proteomics Database

Other Molecular Biology Databases.

•PubMed
•BioModels
•Drugs and drug design
•Molecular probes and primers

Organelle databases.

•Chloroplast Genome Database
•FUGOID
•PLprot
•Mitochondrial genes and proteins

Plant databases.

•Chloroplast Genome Database
•General plant databases
•Arabidopsis thaliana
•Rice

Immunological databases.

•ALPSbase
•AntigenDB
•AntiJen
•BCIpep

Cell Biology.

•BARCdb
•BARD
•CloneDB
•NCBI Bookshelf

Bioinformatics researchers having difficulties to track tools, information and method in field or even within the specialty area.

Biologist user do not have a comprehensive index of bioinformatics algorithm, databases and literature annotation.

Allow biologist user to search what they need easily.

Provide the biologist user with the information about a link's context and narrow down the database best suited to their research need.

The increasing number of databases in the past decade

In the field of biology, make biological data are accessible

Increase in number of publicly available databases.

Provide information that analyse, integrate and summarize the available data.

Provide an invaluable resource for the biological community.

There is a pressing need to store, share, organize, catalogue and rate the resources.

So that the information they contain can be most effectively exploited.

Facilitate the viewer to obtain valuable resource for scientific research.

Each entry is structured using templates and can carry various user comments and annotations.

Entries can be searched, listed, browsed or queried. User-friendly.

Nucleic Acid Sequence and Structure

CEGA

A collection of non-coding sequences that are poorly characterized but highly conserved within various group
of vertebrates.

JuncDE

Databases of exon-exon junction sequences.

dbSUPER, SEA

Collect the sequences of super-enhancer.

Dfam

Databases of human DNA repeat families.

AREsite

Resource of Au-rich elements in vertebrates.

UTRs,NPIDB

Nuclear-protein interaction databases.

JASPAR,HOCOMOCO,ORegAnno,RegulonDB

Databases of transcriptional regulation

BIGNAsim

Databases of DNA dynamics.

Protein Sequence and Structure

pfam, PANTHER, eggNOG,
GPCRdb, TCDB.

Popular protein families databases

MEROPS, Degradome

Databases of proteases and
proteases inhibitor.

ELM, NBDB,
UET.

Databases of protein sequence motifs.

SORF, PRIDE,
dbPTM

Poteomics database.

PDBs, PDBFlex.

Protein structure database.

Metabolic and Signalling Pathways.

KEGG, MetaCyc, Reactome, WikiPathways,
ECMDB, BIGG Models, MNXref, MetaNETX,
Metabolomics Workbench.

Databases of all kinds of metabolomics data, ex: protocols, tutorial and analysis tools.

Viruses, Bacteria, Protozoa,Fungi

BacDive

Coverage of organismal diversity.

MG-RAST,
EBI Metagenomics,
probeBASE,
Human Pan-Microbe communities.

Updates on popular metagenomics resources.

BacWGST

Bacterial whole-genome sequence typing database.

Genome of Human and Model Organisms.

Ensembl, RefSeq, UCSC Genome Browser,
FlyBase, ENCODE Portal Hymenoptera.

Human and model organisms genome resources.

DMDD

Collect phenotypic data of mouse mutant embryos.

dbMAE

Databases of autosomal monoallelic gene expression.

Human Disease and Drugs

ClinVar,
GWASdb,
HaploREG.

Human genetic variation as it relates to disease.

DIDA

Collect data on diseases such as Bardet-Biedl and Kallmann syndromes.

Plants

PlantPromoter Analysis Navigator,
1C4R.

Plant databases.

Others

NCBI's PubChem,
EBI's ChemBI,
SureChemBL.

Databases of chemical, small compounds.

CSDB,
GlyToucan.

Glycoinformatics resourses.

MitoCarta,
MitoMiner,
MitoAge.

Databases of mitochondria protein and properties.

1685 Databases

88 new resources

23 obselete websites.

-The function of previous databases differed from time to time and have been replaced with new databases that are updated for example Families of Structurally Similar Proteins (FSSP) database was superseded by the Dali database.

-Most of the citation in the databases duplicated the same data by the same authors.

-Limited access to only to the registered users for example Human Gene Mutation Database (HGMD).

-The databases are have highly specialized data and/or narrow target audience.

-The ExDom database of exon-intron structures of genes in seven eukaryotic genomes had been removed as it does not provide a free version anymore due to the tightening budget.