1. Importance of NAR
1.1. Users require a bioinformatics tool or database for research purpose.
1.2. They provide an easy-to-use guide to navigate this huge volume and help placing related data next to each other.
1.3. Flexible approach to classify protein structure.
1.4. Useful benchmark for protein documentation.
1.5. The source is always monitored and maintained by respective database coordinator.
1.6. Flexible approach to classify protein structure.
2. Organization of NAR database and its major grouping
2.1. Nucleotide sequence database
2.1.1. International Nucleotide Sequence Database Collaboration
2.1.2. Coding and non-coding DNA
2.1.3. Gene structure, introns and exons, splice sites
2.1.4. Transcriptional regulator sites and transcription factors
2.2. RNA sequence database
2.3. Protein sequence database
2.3.1. General sequence databases
2.3.2. Protein properties
2.3.2.1. HHMD - Human Histone Modification Database
2.3.2.2. TopFIND - Protein N- and C-termini and protease processing
2.3.3. Protein localization and targeting
2.3.3.1. TM Pad - Helix-packing folds in transmembrane proteins
2.3.3.2. Secreted Protein Database - Secreted proteins from human, mouse and rat
2.3.4. Protein sequence motifs and active sites
2.3.4.1. Minimotif Miner - Search tools for short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules.
2.3.4.2. PolyQ - Polyglutamine Repeats in Proteins
2.3.5. Protein domain databases; protein classification
2.3.5.1. BAliBASE - Benchmark database for comparison of multiple sequence alignments.
2.3.5.2. OMA - Orthologous MAtrix: orthology inference among 1000 complete genomes
2.3.6. Databases of individual protein families
2.3.6.1. CLIPZ - Experimentally-determined binding sites of RNA-binding proteins.
2.3.6.2. Heme types, protein structures, axial ligands and Em values
2.3.7. Protein properties
2.4. Structure database
2.4.1. BARD
2.4.2. Small molecules
2.4.2.1. PubChem - Structures and biological activities of small organic molecules.
2.4.2.2. MMsINC - Database of commercially-available compounds for virtual screening and chemoinformatics
2.4.3. Carbohydrates
2.4.3.1. Glycan - Carbohydrate database, part of the KEGG system
2.4.3.2. CSS (Carbohydrate Structure Suite)- Carbohydrate 3D structures derived from the PDB
2.4.4. Nucleic acid structure
2.4.4.1. Greglist - G-quadruplex motifs and potentially G-quadruplex regulated genes
2.4.4.2. Voronoia4RNA - Packing of RNA molecules and complexes
2.4.4.3. G-quadruplex motifs and potentially G-quadruplex regulated genes
2.4.5. Protein structure
2.4.5.1. fPOP - Footprinting protein functional surfaces by comparative patterns
2.4.5.2. Genome3D - Domain structure predictions and 3D models for proteins from model genomes
2.5. Genomic database
2.5.1. MGD - Mouse Genome Database
2.5.2. The Gene Indices
2.5.3. MGD - Mouse Genome Database
2.5.4. Non-verterbrates
2.5.4.1. Genome annotation terms, ontologies and nomenclature
2.5.4.1.1. Example : BioGPS
2.5.4.1.2. Gene annotation portal and a resource on gene and protein function
2.5.4.1.3. Gene Ontology-based functional similarity values for proteins and protein families
2.5.4.2. Taxonomy and identification
2.5.4.2.1. Example : SuperCAT A database for multilocus sequence typing analysis of the Bacillus cereus group of bacteria.
2.5.4.2.2. Example : MetaRef Metagenomic catalog of clade-specific microbial genes
2.5.4.3. General genomic databases
2.5.4.3.1. Example : BacMap Picture atlas of annotated bacterial genomes
2.5.4.3.2. Example : CoGen++ Complete Genome Tracking database
2.5.4.4. Viral genome databases
2.5.4.4.1. Example : ViTa microRNAs targets of the influenza virus
2.5.4.4.2. Example : phiSITE Gene regulation in bacteriophages
2.5.4.5. Prokaryotic genome databses
2.5.4.5.1. Example : DOOR Predicted operons in bacterial and archaeal genomes
2.5.4.5.2. Example : SporeWeb Regulatory pathways during the sporulation cycle of Bacillus subtilis
2.5.4.6. Unicellular eukaryotes genome databases
2.5.4.6.1. Example : pico-PLAZA Genome database of microbial photosynthetic eukaryotes
2.5.4.6.2. Example : metaTIGER Metabolic evolution resource and its application to Plasmodium evolution
2.5.4.7. Fungal genome databases
2.5.4.7.1. Example : GÉnolevures A comparison of S. cerevisiae and 14 other yeast species
2.5.4.7.2. Example : PhenoM Morphological database of essential yeast genes
2.5.4.8. Invertebrate genome databases
2.5.4.8.1. Example : FLIGHT Drosophila phenotypes, gene expression and protein interaction data
2.5.4.8.2. Example : Sebida Sex bias in insect gene expression database
2.6. Metabolic and signaling pathways
2.6.1. Prokaryotic genome databases
2.6.1.1. Example : ProPortal Prochlorococcus marinus and its phages
2.6.1.2. Example : Roundup Orthologs and corresponding evolutionary distances
2.6.2. Enzymes and enzyme nomenclature
2.6.2.1. Example : ExplorEnz Reference database of the IUBMB Enzyme Nomenclature
2.6.2.2. Example : eQuilibrator Thermodynamics calculator for biochemical reactions
2.6.3. Metabolic pathways
2.6.3.1. Example : Bionemo Curated information about biodegradation-related genes and proteins
2.6.3.2. Example : Rhea EBI's biochemical reaction database
2.6.4. Protein-protein interactions
2.6.4.1. Example : Human Protein Interaction database (HPID) Protein interaction predictions by several different methods
2.6.4.2. Example : PepCyber:P~Pep Human protein interactions mediated by phosphoprotein-binding domains
2.6.5. Signalling pathways
2.6.5.1. Example : PhosPhAt Arabidopsis Protein Phosphorylation Site Database
2.6.5.2. Example : KBDOCK Protein domain interactions and interfaces
2.7. Human and other verterbrates genome
2.7.1. Model organisms, comparative genomics
2.7.1.1. Example : cBARBEL Catfish genome database
2.7.1.2. Example : Manteia Embryonic development of the mouse, chicken, zebrafish and human
2.7.2. Human genome databases, maps and viewers
2.7.2.1. Example : Locus Reference Genomic sequences Each LRG is stable genomic DNA sequence for a region of the human genome
2.7.2.2. Example : X:MAP Annotation and visualization of genome structure for Affymetrix exon array analysis
2.7.3. Human ORFs
2.7.3.1. Example : Evola Human genes and their vertebrate orthologs
2.7.3.2. Example : Hoppsigen Human and mouse homologous processed pseudogenes
2.8. Human genes and diseases
2.8.1. General human genetics databases
2.8.1.1. Example : MutDB Predicted biochemical effects of human genetic variation: maping of SNPs on protein sequence and structure.
2.8.1.2. Example : GenAtlas Human genes, markers, and phenotypes
2.8.2. General polymorphism databases
2.8.2.1. Example : Patrocles Polymorphic miRNA-mediated gene regulation in vertebrates.
2.8.2.2. Example : YH database A database for the first Asian diploid genome
2.8.3. Cancer gene databases
2.8.3.1. Example : DriverDB Cancer driver genes/mutations deduced from cancer exome-seq results
2.8.3.2. Example : PubMeth Links between DNA methylation levels and cancer
2.8.4. Gene-, system- or disease-specific databases
2.8.4.1. Example : AutDB Catalog of genes linked to Autism Spectrum Disorders
2.8.4.2. Example : HOX-PRO Clustering of homeobox genes
2.9. Microarray data and other gene expression databases
2.9.1. Example : 4DExpress Database for cross species expression pattern comparisons
2.9.2. Example : LOLA List of lists annotated: a comparison of gene sets identified in different microarray experiments
2.10. Proteomic resources
2.10.1. Example : PeptideAtlas Mass-spectrometry-based proteomics data for human, yeast, E.coli and Mycobacterium
2.10.2. Example : Plasma Proteome Database Qualitative and quantitative information on proteins in human plasma and serum
2.11. Organelle databases
2.11.1. Chloroplast Genome Database
2.11.2. FUGOID
2.11.3. GOBASE
2.11.4. Organelle DB
2.11.5. Organelle genomes
2.11.6. PeroxisomeDB
2.11.7. Plant Organelles Database
2.11.8. PLprot
2.11.9. Mitochondrial genes and proteins
2.12. Plants databases
2.12.1. Chloroplast Genome Database
2.12.2. General plant databases
2.12.3. Arabidopsis thaliana
2.12.4. Rice
2.12.5. Other plants
2.13. Immunological databases
2.13.1. HaptenDB
2.13.2. Protegen
2.13.3. Mitochondrial genes and proteins
2.14. Cell biology
2.14.1. CloneDB
2.14.2. ExoCarta
2.14.3. Example : LUCApedia Predicted genome, proteome, and reactome of LUCA
2.14.4. Example : DNAtraffic DNA dynamics during the cell cycle
2.15. Other molecular databases
2.15.1. Example : CellFinder Gene and protein expression, phenotype and images mapped to the cell types
2.15.2. Example : MetaRouter Compounds and pathways related to bioremediation
2.15.3. Drugs and drug design
2.15.3.1. Example : BioDrugScreen A resource for computational drug design and discovery
2.15.3.2. Example : Transformer Biotransformation of xenobioitics - drugs and food ingredients - by human enzymes
2.15.4. Molecular probes and primers
2.15.4.1. Example : Primer Studio PCR primers for eukaryotic and prokaryotic genes
2.15.4.2. Example : OligoArrayDb Pangenomic sets of microarray probes for organisms with fully sequenced genomes
2.16. Immunological databases
2.16.1. Example : HPTAA Database of potential tumor-associated antigens that uses expression data from various expression platforms, including carefully chosen publicly available microarray expression data, GEO SAGE data and Unigene expression data
2.16.2. Example : IEDB-3D Structural data within the Immune Epitope Database
2.17. Plants databases
2.17.1. General plant databases
2.17.1.1. Example : Phytozome JGI's platform for green plant genomics
2.17.1.2. Example : GoMapMan Unified plant-specific gene ontology
2.18. Organelle databases
2.18.1. Example : PLprot Arabidopsis thaliana chloroplast protein database
2.18.2. Example : Plant Organelle Databases Images of plant organelles and protocols for plant organelle research12
2.18.3. Mitochondrial genes and proteins
2.18.3.1. Example : MitoGenesisDB Expression data to explore spatio-temporal dynamics of mitochondrial biogenesis
2.18.4. Arabidopsis thaliana
2.18.4.1. Example : CATdb Arabidopsis transcriptome data
2.18.4.2. Example : SeedGenes Genes essential for Arabidopsis development
2.18.5. Rice
2.18.5.1. Example : RiceXPro Rice transcriptome under natural conditions
2.18.5.2. Example : OryGenesDB Rice genes, T-DNA and Ds flanking sequence tags
2.18.6. Other plants
2.18.6.1. Example : MedicCyc Biochemical pathways in Medicago truncatula
2.18.6.2. Example : Genome database for Rosaceae Genetics and genomics data on apple, cherry, peach, pear, raspberry, rose and strawberry