Nucleic Acid Research (NAR) Database
The different types of databases that useful in searching information of haemoglobin
Protein sequence databases
General sequence database
NCBI Protein database
1. NCBI provides Global Cross-database Search.
2. Search results for haemoglobin displayed various data types available and those data are nicely categorized into different categories such as literature, organisms, proteins, chemicals and pathways.
3. From the category of proteins, key in haemoglobin. The search results would show approximately 32656 records related to sequences for various haemoglobins, 898 records related to structures, 167 records associated with the sequence similarity-based protein clusters, followed by 16 records related to the conserved protein domains.
Protein properties
BindingDB
1. From the full search results for haemoglobin, various haemoglobin-related assays are available.
2. Provide a deep search for various detailed data related those assays.
3. For example, this database curates measured binding affinities for the association of haemoglobin with various small organic molecules and their inhibition effect respectively.
number available
online molecular biology database collection
1552 online databases
15 major groups
41 subcategories
Criteria for selection into NAR databases
The general utility of the database to the scientific community
Comprehensiveness of coverag
Degree of value added (usually in the form of manual curation) in the production of the database
Web-accessible databases that offer carefully curated data that are not available elsewhere
Freely available online as well as selected databases published elsewhere
Data warehouses, portals, cross-platform search tools and visualization tools
Providing a convenient one-stop source of disparate data not available elsewhere
Supplement with convenient search tools and easy-to-use visualization
Avoid accepting databases on gene expression
as the underlying data must be submitted to array express/ GEO
Avoid accepting new EST databases
particularly those dealing with individual species
as these data have a home in the DDBJ, genbank and European Nucleotide Archive databases
Consideration of so-called ‘boutique’ databases, covering relatively narrow topics
Why we need to group the databases?
To manage an increasing number of informations in the systematic ways
To narrow down the search results
To utilise the databases effectively when neccessary
To track databases, methods and tools in specific field
To exploit the related resources or specific information easily and effectively
To update the changes (deletion and insertion of databases)
Why databases are created and shared?
Emphasis on genome data to improve human health and disease treatment
Comparative genomics purposes between diverse organisms and species
For integration and cross-reference
To prevent loss of resources
As tools for genome analysis
Ensure data available are up-to-date
Why some databases are no longer in the the databases and dropped from it?
Obsolete and non-responsive
Redundancy
Taken commercial route and no free version
Limited budjets
Organisation of databases and its major grouping
Nucleotide Sequence Databases
International Nucleotide Sequence Database Collaboration
Eg. DDBJ-DNA Data Bank of Japan
Eg. GenBank
Eg. NCBI Biosample/ BioProject
Eg. The Sequence Read Archive (SRA)
Coding and non-coding DNA
Eg. MethDB
Eg. Plant repeat database
Eg. TranspoGene
Gene structure, introns and exons, splice sites
Eg. GeneTack
Eg. Spliceosome Database
Transcriptionnal regulator sites and transcription factors
Eg. QuadBase
Eg. TFClass
RNA Sequences Databases
16S and 23S Ribosomal RNA Mutation Database
3D rRNA modification maps
5S Ribosomal RNA Database
Database for Bacterial Group II Introns
HIV Sequence Database
Ribosomal Database Project (RDP-II)
RNA Modification Database
The Small Subunit rRNA Modification Database
Protein Sequences Databases
General sequence databases
Eg. Patome
Eg. UniProt
Protein properties
Eg. BindingDB
Eg. REFOLD
Protein localization and targeting
Eg. CentrosomeDB
Eg. PeroxisomeDB
Protein sequence motifs and active sites
Eg. eBLOCKS
Eg. PHOSIDA
Protein domain databases; protein classification
Eg. FunShift
Eg. OrthoDB
Databases of individual protein families
Eg. BACTIBASE
Eg. Histone Database
Eg. TransportDB
Eg. SuperCYP
Structural Databases
Small molecules
Eg. ChemBank
Eg. DrugBank
Eg. SuperDrug
Eg. SuperToxic
Carbohydrates
Eg. GlycoMapsDB
Eg. Monosaccharide Browser
Nucleic acid structure
Eg. 3DNALandscapes
Eg. QuadBase
Eg. RNA FRABASE
Protein structure
Eg. DSDBASE
Eg. IDEAL
Eg. SitesBase
Genomics Databases (non-vertebrate)
Genome annotation terms, ontologies ad nomenclature
Eg. BioThesaurus
Eg. IUPAC Nomenclature database
Eg. MetaBase
Taxonomy and identification
Eg. GeneTrees
Eg. MetaRef
General genomics databases
Eg. BacMap
Eg. GenoList
Viral genome databases
Eg. HepSeq
Eg. HIV Drud Resistance Database
Prokaryotic genome databases
Eg. AlterORF
Eg. MicroScope
Unicellular eukaryotes genome databases
Eg. Camparasite
Eg. TBestDB
Fungal genome databases
Eg. YeastNet
Eg. YEASTRACT
Invertebrate genome databases
Eg. NEMBASE
Metabolic and Signaling Pathways
Prokaryotic genome databases
Eg. NMPDR-National Microbial pathogen Data Resource
Enzymes and enzymes nomenclature
Eg. FunTree
Eg. MultiTaskDB
Metabolic pathwaqys
Eg. Bionemo
Eg. Reactom
Protein-protein interaction
Eg. EndoNet
Eg. GeneNet
Eg. VirusMINT
Eg. SynSysNet
Signalling pathway
Eg. Networkin
Eg. Quorumpeps
Eg. SPIKE
Human and other Vertebrate Genomes
Model organisms, comparative genomics
Eg. Animal Genome Size Database
Eg. Mouse Phenome Database
Eg. TreeFam
Human genome databses, maps and viewers
Eg. GeneAnnot
Eg. GeneLoc
Human ORFs
Eg. GeneSpeed
Eg. PlasmID
Eg. PReMod
Human Genes and Diseases
General human genetics databases
General polymorphism databases
Cancer gene databases
Gene-, system-, disease-specific databases
Microarray Data andother Gene Expression Databases
Eg. CycleBase
Eg:Gene Expression Barcode
Eg. GeneNote
Eg. GeneTrap
Proteomics Databases
Eg. 2D-PAGE
Eg. PeptideAtlas
Other Molecular Biology Databases
Drugs and drug design
Eg. BacMet
Eg. SuperNatural
Molecular probes and primers
Human OligoGenome Resource
PrimerBank
probeBase
RTPrimerDB
Eg. BioModels
Eg. PubMed
Organelle Databases
Mitochondrial genes and proteins
Eg. Human MtDB
Eg. MitoDrome
Eg. MitoGenesisDB
Eg. Organelle DB
Eg. Organelle genomes
Eg. Plant Organelles Databases
Plant Databases
General plant databases
Eg. GeneFarm
Eg. MetaCrop
Arabidopsis thaliana
Rice
Other plants
Eg. Chloroplast Genome Database
Immunological Databases
Eg. AntigenDB
Eg. Epitome
Eg. Protegen
Eg. The Immune Epitope Database (IEDB
Cell Biology
Eg. CloneDB
Eg. ExoCarta
Eg. MethylomeDB
Eg. NCBI Bookshelf