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Category:Databases
From EcoliWiki
This category deals with different online databases containing information related to E. coli K-12 and other genomics information.
To add a new database page to this category, fill in the title of the Database and click "Create":
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| Database | Content | Documentation |
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| 2DBase | 2D-PAGE database of Escherichia coli | EcoliWiki page |
| 5S rRNA Database | Information on nucleotide sequences of 5S rRNAs and their genes | EcoliWiki page |
| Addgene Vectorpedia | Searchable database of plasmid vectors. Despite the name, Vectorpedia does not appear to be a wiki | EcoliWiki page |
| AlignACE | Matrices which search for additional binding sites in the E. coli genomic sequence. | EcoliWiki page |
| ArrayExpress | Public repository for microarray data | EcoliWiki page |
| ASAP | Comprehensive genome information for several enteric bacteria with community annotation. | EcoliWiki page |
| A CLassification of Mobile Genetic Elements (ACLAME) | Comprehensive database of prokaryotic Mobile Genetic Elements | EcoliWiki page |
| Bacteriome | An integrated protein interaction database for E. coli. Bacteriome features a high quality functional interaction dataset of E. coli proteins togther with experimental datasets generated through tandem affinity purification screens. | EcoliWiki page |
| BeeBase | Apis mellifera Genome Resources | EcoliWiki page |
| BioGPS | Gene portal hub | EcoliWiki page |
| Biomodels | Allows you to store, search and retrieve published mathematical models of biological interests. | EcoliWiki page |
| BRENDA | Comprehensive enzyme information database. | EcoliWiki page |
| BSGI | BSGI: Bacterial Structural Genomics Initiative | EcoliWiki page |
| CATH | Protein Structure Classification | EcoliWiki page |
| CBS Genome Atlas | CBS Genome Atlas | EcoliWiki page |
| Center for Information Biology Gene Expression Database (CIBEX) 2 | Center for Information Biology Gene Expression Database | EcoliWiki page |
| CGD | Candida Genome Database | EcoliWiki page |
| CheBi | Chemicals of Biological Interest | EcoliWiki page |
| COGs | Phylogenetic classification of proteins encoded in complete genomes | EcoliWiki page |
| ColiBASE | A database for comparative genome analysis of Enterobactericaiae. | EcoliWiki page |
| Colibri | Provides a complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12, linked to the relevant annotations and functional assignments. | EcoliWiki page |
| Comprehensive Microbial Resource (CMR) | Information on all of the publicly available, complete prokaryotic genomes. | EcoliWiki page |
| Conserved Domain Database (CDD) | EcoliWiki page | |
| CoryneRegNet | A reference database for corynebacterial gene regulatory networks. | EcoliWiki page |
| CoSMoS | Conserved Motif Search: CoSMoS is a database of alignments of all Escherichia coli proteins with their homologues in 2780 different species found in the NCBI RefSeq (release 9) database | EcoliWiki page |
| CyberCell | Collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli K-12 MG1655. | EcoliWiki page |
| DictyBase | An Online Informatics Resource for Dictyostelium | EcoliWiki page |
| Doodle | A database of experimentally determined protein oligomerization domains. | EcoliWiki page |
| E. coli Database Collection (ECDC) | Information regarding the entire E.coli K12 chromosome | EcoliWiki page |
| E. coli Entry Point | E. coli functional annotation | EcoliWiki page |
| E. coli Genetic Stock Center (CGSC) | Coli Genetic Stock Center; strains and genetic information | EcoliWiki page |
| E. coli Genome Project at UW-Madison | Annotations of the E. coli K-12 genome and its annotations. Creating knockouts of every gene, clone of every ORF, and extensive gene expression under varying physiological conditions. | EcoliWiki page |
| E. coli Reference Center | Largest repository for environmental E. coli strains in America. | EcoliWiki page |
| ECCE | E. coli Cell Envelope Proteins | EcoliWiki page |
| EchoBASE | Curated experimental and bioinformatic information about E. coli genes and gene products | EcoliWiki page |
| EciD | For exploring the sizeable amount of protein interaction-related data available for Escherichia coli | EcoliWiki page |
| EcoCyc | Comprehensive database of E. coli molecular components | EcoliWiki page |
| ECODAB | Escherichia coli O-antigen Database | EcoliWiki page |
| EcoGene | EcoGene, comprehensive data resource for E. coli | EcoliWiki page |
| EcoliHub | Comprehensive data resource for E. coli K-12 and its phage, plasmids, and mobile genetic elements. | EcoliWiki page |
| EcoliWiki | Wiki-based community annotation for ''E. coli'' K-12, as part of [http://ecolihub.org EcoliHub] | EcoliWiki page |
| EcoProDB | Integrates protein information identified on 2-D gels along with other resources. | EcoliWiki page |
| ECOR | A reference collection of E. coli strains found in nature | EcoliWiki page |
| EcoSal | Review articles on topics related to E. coli and Salmonella | EcoliWiki page |
| Ehrmann | EcoliWiki page | |
| eNet | Gene function prediction and annotation of ''Escherichia coli'' K12 proteins using physical protein-protein interactions, genomic context methods and machine learning algorithms | EcoliWiki page |
| Ensembl Compara | A genome databases for vertebrates and other eukaryotic species | EcoliWiki page |
| ERIC | Enteropathogen Resource Integration Center | EcoliWiki page |
| Escherichia coli transcription factor binding sites (TFBS) | Transcription Factor Binding Sites | EcoliWiki page |
| Eukaryotic Pathogens Database Resources (EuPathDB) | A portal for accessing genomic-scale datasets associated with the eukaryotic pathogens. | EcoliWiki page |
| European Bioinformatics Institute (EBI) | European Bioinformatics Institute main page | EcoliWiki page |
| Euro rRNA db | Compiles all complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences in aligment format. | EcoliWiki page |
| ExPASy proteomics server | Analysis of protein sequences and structures. | EcoliWiki page |
| Faculty of 1000 | Highlights and reviews of papers in the biological sciences recommended as interesting by members of the Faculty of 1000. | EcoliWiki page |
| FAMSBASE | Protein structure models by homology modeling | EcoliWiki page |
| Fellowship for the Interpretation of Genomes (FIG) | Analysis of subsystems across multiple genomes | EcoliWiki page |
| FlyBase | Genetic and molecular data for D. melanogaster and other Drosophila species. | EcoliWiki page |
| FusionDB | Prokaryotic gene fusion events | EcoliWiki page |
| GenExpDB | ''E. coli'' Gene Expression Database | EcoliWiki page |
| Gene Expression Omnibus (GEO) | NCBI archive of expression data | EcoliWiki page |
| Gene Ontology (GO) | Provides a controlled vocabulary to describe gene and gene product attributes in any organism. | EcoliWiki page |
| GenoBase | Public repository for Sequence Information, Proteome, Transcriptome, Bioinformatics, and Knowledge based on literature concerning E. coli. | EcoliWiki page |
| Genome Information Broker (GIB) | Comprehensive database of complete microbial genomes | EcoliWiki page |
| Genomic tRNA database | Genomic tRNA database contains tRNA gene predictions made by the program tRNAscan-SE. | EcoliWiki page |
| GenProtEC | Functions encoded by the Escherichia coli K-12 | EcoliWiki page |
| GIRC | Microbial Gene Products | EcoliWiki page |
| GMOD | An open source project for creating and managing genome-scale biological databases. See the [http://gmod.org/wiki/Overview project overview] for more. | EcoliWiki page |
| GONUTS | Gene Ontology Normal Usage Tracking System (GONUTS) Community curation of usage notes for GO and GO annotations for genes | EcoliWiki page |
| GTOP | Data analyses of proteins, sequence homology analyses, and three-dimensional structures of proteins. | EcoliWiki page |
| High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) | UniProt/ExPASY component | EcoliWiki page |
| Information Hyperlinked Over Proteins (IHOP) | A way of accessing millions of PubMed abstracts. | EcoliWiki page |
| InParanoid | Eukaryotic Ortholog Groups | EcoliWiki page |
| IntAct | Database of protein-protein interactions derived from literature curation or direct user submissions. | EcoliWiki page |
| Integrated Microbial Genomes | Joint Genome Intstitute's Microbial Genomes | EcoliWiki page |
| IntEnz | IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. | EcoliWiki page |
| International Committee on Taxonomy of Viruses (ICTVdB) | Virus database | EcoliWiki page |
| Interoperation | EcoliWiki page | |
| InterPro | EcoliWiki page | |
| Isfinder | List of insertion sequences isolated from eubacteria and archae. | EcoliWiki page |
| JGI Microbial Genomics | Joint Genome Institute Microbial Genomes site | EcoliWiki page |
| Kyoto Encyclopedia of Genes and Genomes (KEGG) | Encyclopedia of Genes, Genomes, and Pathways | EcoliWiki page |
| Many Microbe Microarrays Database (M3D) | Affymetrix data for ''E. coli'' and other bacteria | EcoliWiki page |
| Membrane Protein Data Bank (MPDB) | A database for membrane proteins | EcoliWiki page |
| MEROPS | Resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. | EcoliWiki page |
| MetaBase | A Database of Databases | EcoliWiki page |
| Microbes Online | EcoliWiki page | |
| Microbe Project | A Portal to U.S. Federal efforts in microbial research. | EcoliWiki page |
| Microbial Signal Transduction (MiST) | Signal transduction proteins from bacteria and archaea. | EcoliWiki page |
| ModBase | 3-dimensional protein models from comparative modeling | EcoliWiki page |
| Mouse Genome Informatics (MGI) | Integrated access to data on the genetics, genomics and biology of the laboratory mouse | EcoliWiki page |
| Mycozome | A database for the comparative studies of fungal genomes. | EcoliWiki page |
| National Food Safety %26 Toxicology Center | Information about E. coli food pathogens | EcoliWiki page |
| NCBI | National Center for Biotechnology Information | EcoliWiki page |
| NCBI Short Read Archive | Repository of reads from high-throughput sequencing at NCBI | EcoliWiki page |
| Neurospora at MIPS | Database for the molecular structure and functional network of Neurospora crassa. | EcoliWiki page |
| NHGRI | National Human Genome Reasearch Institute | EcoliWiki page |
| NONCODE | noncoding RNA database | EcoliWiki page |
| Noncoding RNA database | A database that provide information on the sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell. | EcoliWiki page |
| OpenWetWare | Wiki-based collection of lab websites, with information on materials, protocols, and courses. | EcoliWiki page |
| Open Biosystems | A service to distribute biological resources, especially genome scale sets | EcoliWiki page |
| OrthoMCL-DB | A genome-scale algorithm for grouping orthologous protein sequences. | EcoliWiki page |
| PEC | Profiling ''E. coli'' Chromosome PEC focuses on gene function | EcoliWiki page |
| Pedro%27s molecular biology tools | EcoliWiki page | |
| PGD | Collate biological and genomic data for all bacterial plasmids for interrogation of both meta- and genomic data. | EcoliWiki page |
| phiSITE | Database of Gene Regulation in Bacteriophages | EcoliWiki page |
| PHOSIDA | Phosida - Phosphorylation Site Database | EcoliWiki page |
| Phylogenomic Display of Bacterial Genes (Phydbac) | Phylogenomic Display of Bacterial Genes (Phydbac) | EcoliWiki page |
| PhylomeDB | A database for genome-wide collections of gene phylogenies. | EcoliWiki page |
| Pittsburgh Bacteriophage Institute | Sequences of bacteriophages determined in at Pitt (as well as sequences of other notable phages), publications, and much more. | EcoliWiki page |
| PMTG | E. coli short DNA repeats, super integrons, ABC transporters, and genomic toxicology | EcoliWiki page |
| PQS | Predicted quaternary structure for structures deposited at the PDB | EcoliWiki page |
| Princeton Protein Orthology Database (P-POD) | Princeton Ortholog Database | EcoliWiki page |
| ProDOM | ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database. | EcoliWiki page |
| ProtCom | A collection of protein-protein homo- and hetero-complexes as well as domain-domain structures. | EcoliWiki page |
| Protein Data Bank (PDB) | RCSB Protein Data Bank. | EcoliWiki page |
| Protein Feature Ontology | EcoliWiki page | |
| Protein Information Resource (PIR) | Protein sequences and functional information | EcoliWiki page |
| Protein Link Explorer (PLEX) | Protein Link Explorer | EcoliWiki page |
| Proteopedia | Wiki based information about protein structures | EcoliWiki page |
| ProTherm | A collection of numerical data of thermodynamic parameters for wild type and mutant proteins. | EcoliWiki page |
| Pseudomonas Genome Database | Pseudomonas aeruginosa genome information | EcoliWiki page |
| PubMed | Search peer-reviewed literature by keyword. | EcoliWiki page |
| Rate Limiting Enzymes Database (RLEdb) | A central repository of metabolic rate-limiting enzymes as well as their regulatory information include their related transcriptional factors, reversible phosphorylation sites and inhibitors. | EcoliWiki page |
| Reactome | Open-source, curated resource of core pathways and reactions in human biology. | EcoliWiki page |
| REFOLD | Database of refolding protocols for protein purification | EcoliWiki page |
| RefSeq | EcoliWiki page | |
| RegTransBase | A database of regulatory sequences and interactions in a wide range of prokaryotic genomes | EcoliWiki page |
| RegulonDB | RegulonDB provides information on operon organization and regulation in ''E. coli.'' | EcoliWiki page |
| RFam | RFam - RNA families | EcoliWiki page |
| Ribosomal Protein Gene Database (RPG) | Ribosomal protein gene orthologs from different prokaryotes and eukaryotes | EcoliWiki page |
| RNAmods | Comprehensive listing of post-transcriptionally modified nucleosides from RNA | EcoliWiki page |
| RoundUp - Orthology Database | A database of orthologs and corresponding evolutionary distances. | EcoliWiki page |
| SCOR | A database that provides understanding of RNA motif structure, function, tertiary interactions and their relationships. | EcoliWiki page |
| SDSU Microbial Informatics Group | EcoliWiki page | |
| Sequence Ontology | Sequencing annotation data. | EcoliWiki page |
| SGD | Comprehensive data resource for ''S. cerevisiae'' (baker's yeast) | EcoliWiki page |
| SHIGEN | Shared Information of Genetic Resources | EcoliWiki page |
| sRNAMap | Small noncoding RNA Map | EcoliWiki page |
| Stanford MicroArray Database | The Stanford Microarray Database (SMD is a research tool and archive that allows researchers to store, annotate, analyze and share data generated by high-throughput genomics technology, especially microarrays. | EcoliWiki page |
| Structural Classification of Proteins (SCOP) | Structural Classification of Proteins | EcoliWiki page |
| Structural Proteomics Experimental Database (SPEX) | EcoliWiki page | |
| SubtiList | Database that analyzes the genome of Bacillus subtilis. | EcoliWiki page |
| SwedCAD Database | A database of annotated high-mass accuracy MS/MS spectra of tryptic peptides | EcoliWiki page |
| Swiss-model | Protein structure modeling tool and repository of models | EcoliWiki page |
| T4-like genome database | Genome information about T4-like bacteriophage | EcoliWiki page |
| TDR Targets Database | Searchable database for drug targets for tropical diseases | EcoliWiki page |
| The Arabidopsis Information Resource (TAIR) | TAIR is the model organism database for Arabidopsis thaliana. | EcoliWiki page |
| tmRNA website | Searchable list of tmRNA | EcoliWiki page |
| TOPSAN | Community annotation of protein structures determined by structural genomics centers | EcoliWiki page |
| TreeFam | Tree families database | EcoliWiki page |
| TubercuList | TubercuList provides a complete dataset of DNA and protein sequences derived from the strain ''M. tuberculosis'' H37Rv. | EcoliWiki page |
| UniProt | Comprehensive protein resource | EcoliWiki page |
| VectorDB | Information about cloning vectors | EcoliWiki page |
| Web of Science | Search tools for scientific literature (subscription required) | EcoliWiki page |
| WikiPathways | WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. | EcoliWiki page |
| WikiProteins | EcoliWiki page | |
| WormBase | C. elegans genome information | EcoliWiki page |
| XanthusBase | Myxococcus xanthus genome information | EcoliWiki page |
| Zebrafish Information Network (ZFIN) | Zebrafish Information Network (ZFIN) | EcoliWiki page |
See Also
Subcategories
This category has the following 21 subcategories.
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Pages in category "Databases"
The following 162 pages are in the current category.
