Database Description Reference
  Nucleotide Databases  
DNA Data Bank of Japan It is the member of International Nucleotide Sequence Databases (INSD) and is one of the biggest resources for nucleotide sequences. [37]
European Nucleotide Archive It captures and presents information relating to experimental workflows that are based around nucleotide sequencing. [126]
GenBank It is the member of International Nucleotide Sequence Databases (INSD) and is a nucleotide sequence resource. [47]
Rfam A collection of RNA families, represented by multiple sequence alignments [54]
  Protein Databases  
Uniprot One of the largest collection of protein sequences. [45]
Protein Data Bank This is another major resource of proteins containing information of experimentally-determined structures of nucleic acids, proteins, and other complex assemblies. [38]
Prosite Provides information on protein families, conserved domains and actives sites of the proteins. [43]
Pfam Collection of protein families [39]
SWISS PROT A section of the UniProt Knowledgebase containing the manually annotated protein sequences [32].
InterPro Describes the protein families, conserved domains and actives sites [127]
Proteomics Identifications Database A public source, containing supporting evidence for functional characterization and post-translation modification of proteins and peptides. [128]
  Genome databases  
Ensembl It is a database containing annotated genomes of eukaryotes including human, mouse and other vertebrates. [129]
PIR An integrated public resource to support genomic and proteomic research [34]
  Miscellaneous Databases  
Medherb Resource database for medicinally important herbs [130]
Reactome A peer-reviewed resource of human biological processes [131]
TextPresso This database provides full text literature searches of model organism research, helps database curators to identify and extract biological entities which include new allele and gene names and human disease gene orthologs
TAIR The Arabidopsis Information Resource (TAIR) maintains adatabaseof genetic andmolecular datafor the model plantArabidopsis thaliana. It provides information on gene structure, gene product, gene expression, DNA and seed stocks, genome maps, genetic and physical markers.
dictyBase dictyBaseis an online bioinformatics database for Dictyosteliumdiscoideum. [132]
  Signalling & Metabolic Pathway Databases  
KEGG KEGG is a suite of databases and associated software for understanding and simulating higher-order functional behaviours of the cell or the organism from its genome information. [133]
CMAP Complement Map Database is a novel and easily accessible research tool to assist the complement community and scientists from related disciplines in exploring the complement network and discovering new connections. [134]
SGMP The Signaling Gateway Molecule Pages (SGMP) database provides highly structured data on proteins which exist in different functional states participating in signal transduction pathways. [135]
PID The Pathway Interaction Database (PID) is a collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes. It serves as a research to study the cellular pathways with a special emphasis on cancer. [136]
HMDB The Human Metabolome Database (HMDB) is the most comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases along an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) from the analyses performed on urine, blood and cerebrospinal fluid samples. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. [137]
Table 3: List of some popular databases.