Primary sequence databases

The International Nucleotide Sequence Database (INSD) (http://www.insdc.org/) consists of the following databases. 1. 2. DDBJ (DNA Data Bank of Japan) EMBL Nucleotide Sequence DB (European Molecular Biology Laboratory) 3. GenBank [1] (National Center for Biotechnology Information)

The three databases, DDBJ (Japan), GenBank (USA) and EMBL Nucleotide Sequence Database (Europe), are repositories for nucleotide sequence data from all organisms. All three databases accept nucleotide sequence submissions, and then exchange new and updated data on a daily basis to achieve optimal synchronisation between them. These three databases are primary databases, as they house original sequence data.

[edit]Metadatabases
Strictly speaking a metadatabase can be considered a database of databases, rather than any one integration project or technology. They collect data from different sources and usually make them available in new and more convenient form, or with an emphasis on a particular disease or organism. 1. 2. 3. 4. 5. Entrez[2] (National Center for Biotechnology Information) euGenes (Indiana University) GeneCards (Weizmann Inst.) SOURCE (Stanford University) mGen containing four of the world biggest databases GenBank, Refseq, EMBL and DDBJ - easy and simple program friendly gene extraction 6. Bioinformatic Harvester[3] (Karlsruhe Institute of Technology) Integrating 26 major protein/gene resources. 7. MetaBase[4] (KOBIC) - A user contributed database of biological databases. 8. ConsensusPathDB - A molecular functional interaction database, integrating information from 12 other databases. 9. PathogenPortal A repository linking to the Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID)

10. BioGraph (University of Antwerp, Vlaams Instituut voor Biotechnologie) A knowledge discovery service based on the integration of over 20 heterogeneous biomedical knowledge bases

[edit]Genome

databases

These databases collect organism genome sequences, annotate and analyze them, and provide public access. Some add curation of experimental literature to improve computed annotations. These databases may hold many species genomes, or a single model organism genome. 1. 2. 3. 4. 5. Bioinformatic Harvester SNPedia CAMERA Resource for microbial genomics and metagenomics Corn, the Maize Genetics and Genomics Database EcoCyc a database that describes the genome and the biochemical machinery of the model organism E. coli K-12 6. Ensembl provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes. 7. 8. 9. PATRIC, the PathoSystems Resource Integration Center Flybase, genome of the model organism Drosophila melanogaster MGI Mouse Genome (Jackson Lab.)

10. JGI Genomes of the DOE-Joint Genome Institute provides databases of many eukaryote and microbial genomes. 11. National Microbial Pathogen Data Resource. A manually curated database of annotated genome data for the pathogens Campylobacter, Chlamydia, Chlamydophila, Haemophilus, Lis teria, Mycoplasma, Neisseria, Staphylococcus,Streptococcus, Treponem a, Ureaplasma, and Vibrio. 12. Saccharomyces Genome Database, genome of the yeast model organism. 13. Viral Bioinformatics Resource Center Curated database containing annotated genome data for eleven virus families. 14. The SEED platform for microbial genome analysis includes all complete microbial genomes, and most partial genomes. The platform is used to annotate microbial genomes using subsystems.

15. Xenbase, genome of the model organism Xenopus tropicalis and Xenopus laevis 16. Wormbase, genome of the model organism Caenorhabditis elegans 17. Zebrafish Information Network, genome of this fish model organism. 18. TAIR, The Arabidopsis Information Resource. 19. UCSC Malaria Genome Browser, genome of malaria causing species (Plasmodium falciparumata and others) 20. RGD Rat Genome Database: Genomic and phenotype data for Rattus norvegicus 21. [5] INTEGRALL: Database dedicated to integrons, bacterial genetic elements involved in the antibiotic resistance 22. Fourmidable ant genome database provides ant genome blast search and sequence download. 23. VectorBase The NIAID Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens

[edit]Protein

sequence databases
1. UniProt[6] Universal Protein Resource (UniProt Consortium: EBI, Expasy, PIR) 2. PIR Protein Information Resource (Georgetown University Medical Center (GUMC)) 3. 4. Swiss-Prot[7] Protein Knowledgebase (Swiss Institute of Bioinformatics) PEDANT Protein Extraction, Description and ANalysis Tool (Forschungszentrum f. Umwelt & Gesundheit) 5. 6. 7. PROSITE Database of Protein Families and Domains DIP Database of Interacting Proteins (Univ. of California) Pfam Protein families database of alignments and HMMs (Sanger Institute) 8. PRINTS PRINTS is a compendium of protein fingerprints (Manchester University) 9. ProDom Comprehensive set of Protein Domain Families (INRA/CNRS)

10. SignalP 3.0 Server for signal peptide prediction (including cleavage site prediction), based on artificial neural networks and HMMs

11. SUPERFAMILY Library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms 12. Annotation Clearing House a project from the National Microbial Pathogen Data Resource

[edit]Protein

structure databases
1. Protein Data Bank[8] (PDB) (Research Collaboratory for Structural Bioinformatics (RCSB)) 2. 3. SCOP Structural Classification of Proteins CATH Protein Structure Classification

[edit]Protein

model databases
1. 2. SWISS-MODEL Server and Repository for Protein Structure Models ModBase Database of Comparative Protein Structure Models (Sali Lab, UCSF) 3. Protein Model Portal[9] (PMP) Meta database that combines several databases of protein structure models (Biozentrum, Basel, Switzerland)

[edit]Carbohydrate

structure databases
1. EuroCarbDB[10], A repository for both carbohydrate sequences/structures and experimental data.

[edit]Protein-protein

interactions
1. BioGRID [11] A General Repository for Interaction Datasets (Samuel Lunenfeld Research Institute) 2. STRING: STRING is a database of known and predicted protein-protein interactions. (EMBL) 3. 4. 5. 6. DIP Database of Interacting Proteins BIND Biomolecular Interaction Network Database NetPro CCSB Interactome

[edit]Signal

transduction pathway databases

Cancer Cell Map Netpath - A curated resource of signal transduction pathways in humans

 [edit]Metabolic

Reactome NCI-Nature Pathway Interaction Database SignaLink Database WikiPathways

pathway databases
1. 2. 3. 4. BioCyc Database Collection including EcoCyc and MetaCyc KEGG PATHWAY Database[12] (Univ. of Kyoto) MANET database [13] (University of Illinois) Reactome[14] (Cold Spring Harbor Laboratory, EBI, Gene Ontology Consortium)

[edit]Microarray

databases

Main article: Microarray databases 1. 2. ArrayExpress (European Bioinformatics Institute) Gene Expression Omnibus (National Center for Biotechnology Information) 3. 4. 5. GPX(Scottish Centre for Genomic Technology and Informatics) maxd (Univ. of Manchester) Stanford Microarray Database (SMD) (Stanford University)

[edit]Mathematical

model databases
1. 2. Biomodels Database CellML

[edit]PCR

/ real time PCR primer databases

1. PathoOligoDB: A free QPCR oligo database for pathogens

[edit]Specialized

databases

Antibody Central Antibody information database and search resource. BIOMOVIE (ETH Zurich) movies related to biology and biotechnology CGAP Cancer Genes (National Cancer Institute) Clone Registry Clone Collections (National Center for Biotechnology Information)

Connectivity map Transcriptional expression data and correlation tools for drugs

CTD The Comparative Toxicogenomics Database describes chemical-genedisease interactions

DBGET H.sapiens (Univ. of Kyoto) DiProDB A database to collect and analyse thermodynamic, structural and other dinucleotide properties.

Drug2Gene Provides integrated information for identified and reported relations between genes/proteins and drugs/compounds

Dryad a repository of data underlying scientific publications in the basic and applied biosciences.

Edinburgh Mouse Atlas GreenPhylDB (A phylogenomic database for plant comparative genomics) GDB Hum. Genome Db (Human Genome Organisation) HGMD disease-causing mutations (HGMD Human Gene Mutation Database) HUGO (Official Human Genome Database: HUGO Gene Nomenclature Committee)

HvrBase++ Human and primate mitochondrial DNA INTERFEROME The Database of Interferon Regulated Genes List with SNP-Databases Minimotif Miner -Database of short contiguous functional peptide motifs NCBI-UniGene (National Center for Biotechnology Information) Oncogenomic databases A compilation of databases that serve for cancer research.

OMIM Inherited Diseases (Online Mendelian Inheritance in Man) OrthoMaM (A database of Orthologous Mammalian Markers) p53 The p53 Knowledgebase PhenCode linking human mutations with phenotype PhenomicDB multi-organism database linking genotype to phenotype Plasma Proteome Database Human plasma proteins along with their isoforms PolygenicPathways Genes and risk factors implicated in Alzheimer's disease, Bipolar disorder, Autism or Schizophrenia, multiple sclerosis and Parkinson's disease

SHMPD The Singapore Human Mutation and Polymorphism Database

SciClyc An Open-access database to shared antibodies, cell cultures, and documents for biomedical research.

SNPSTR database A database of SNPSTRs - compound genetic markers consisting of a microsatellite (STR) and one tightly linked SNP - in human, mouse, rat, dog and chicken.

TDR Targets A chemogenomics database focused on drug discovery in tropical diseases.

TRANSFAC A database about eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles.

TreeBASE An open-access database of phylogenetic trees and the data behind them

XTractor Discovering Newer Scientific Relations Across PubMed Abstracts. A tool to obtain manually annotated relationships for Proteins, Diseases, Drugs and Biological Processes as they get published in PubMed.

[edit]Wiki-style

databases
1. 2. 3. 4. 5. 6. 7. 8. 9. CHDwiki EcoliWiki Gene Wiki GyDB OpenWetWare PDBWiki Proteopedia Topsan WikiGenes

10. WikiPathways 11. WikiProfessional 12. YTPdb

[edit]References

1.

^ Wren JD, Bateman A (2008). "Databases, data tombs and dust in the wind.". Bioinformatics 24 (19): 2127 8. doi:10.1093/bioinformatics/btn464. PMID 18819940.

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