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Category:Databases

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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":

DatabaseContentDocumentation
2DBase2D-PAGE database of Escherichia coliEcoliWiki page
5S rRNA DatabaseInformation on nucleotide sequences of 5S rRNAs and their genesEcoliWiki page
AgBaseDatabase for gene products from agricultural organisms.EcoliWiki page
AlignACEMatrices which search for additional binding sites in the E. coli genomic sequence.EcoliWiki page
All the Virology on the WWWAll the Virology on the WWW has information pertaining to viruses and phage.EcoliWiki page
American Biological Safety AssociationAmerican Biological Safety AssociationEcoliWiki page
American Society for Clinical PathologyAmerican Society for Clinical PathologyEcoliWiki page
Animal ToxinAnimal Toxin DatabaseEcoliWiki page
ArrayExpressPublic repository for microarray dataEcoliWiki page
ASAPComprehensive genome information for several enteric bacteria with community annotation. EcoliWiki page
A CLassification of Mobile Genetic Elements (ACLAME)Comprehensive database of prokaryotic Mobile Genetic ElementsEcoliWiki page
BacteriomeAn 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
Bactibaseis a data repository of bacteriocin natural antimicrobial peptides EcoliWiki page
BeeBaseApis mellifera Genome ResourcesEcoliWiki page
BiGG DatabaseEcoliWiki page
BioCartaBioCartaEcoliWiki page
BioDIGBioDIG:Biological Database of Images and GenomesEcoliWiki page
BioGPSGene portal hubEcoliWiki page
BioGRIDEcoliWiki page
Biology ScholarsBiology ScholarsEcoliWiki page
BiomodelsAllows you to store, search and retrieve published mathematical models of biological interests.EcoliWiki page
BioQuest Curriculum ConsortiumBioQuest Curriculum ConsortiumEcoliWiki page
Brede Wiki"Brede Wiki is a wiki with structured information from neuroscience. It contains primarily information from published peer-reviewed neuroimaging articles."EcoliWiki page
BRENDAComprehensive enzyme information database.EcoliWiki page
BSGIBSGI: Bacterial Structural Genomics InitiativeEcoliWiki page
C3Cyberlearning at Community CollegesCyberlearning at Community CollegesEcoliWiki page
CATHProtein Structure ClassificationEcoliWiki page
CBS Genome AtlasCBS Genome AtlasEcoliWiki page
Center for Information Biology Gene Expression Database (CIBEX) 2Center for Information Biology Gene Expression DatabaseEcoliWiki page
CGDCandida Genome DatabaseEcoliWiki page
CheBiChemicals of Biological InterestEcoliWiki page
Ciliate Genomics ConsortiumCiliate Genomics ConsortiumEcoliWiki page
Codon Usage DatabaseCodon Usage DatabaseEcoliWiki page
COGsPhylogenetic classification of proteins encoded in complete genomesEcoliWiki page
ColiBASEA database for comparative genome analysis of Enterobactericaiae.EcoliWiki page
ColibriProvides 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
CollecTF[http://collectf.umbc.edu CollecTF]compiles data on experimentally validated, naturally occurring TF-binding sites across the Bacteria domain, placing a strong emphasis on the transparency of the curation process, the quality and availability of the stored data and fully customizable access to its records.EcoliWiki page
COLOMBOS'''COL'''lection '''O'''f '''M'''icroarrays for '''B'''acterial '''O'''rganism'''S''' Gene expression for E. coli and other model bacteriaEcoliWiki page
Comprehensive Microbial Resource (CMR)Information on all of the publicly available, complete prokaryotic genomes. EcoliWiki page
Conserved Domain Database (CDD)EcoliWiki page
CoryneRegNetA reference database for corynebacterial gene regulatory networks.EcoliWiki page
CoSMoSConserved 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) databaseEcoliWiki page
CyberCellCollection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli K-12 MG1655.EcoliWiki page
Database of prOkaryotic OpeRonsDOOR: the '''D'''atabase of pr'''O'''karyotic '''O'''pe'''R'''ons Operon predictions for 971 complete archeal and bacterial genomes that include both chromosomal and plasmid gene pairs.EcoliWiki page
DBSublocSubcellular localization of ProteinsEcoliWiki page
DictyBaseAn Online Informatics Resource for DictyosteliumEcoliWiki page
DoodleA database of experimentally determined protein oligomerization domains.EcoliWiki page
E. coli Database Collection (ECDC)Information regarding the entire E.coli K12 chromosomeEcoliWiki page
E. coli Entry PointE. 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-MadisonAnnotations 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 CenterLargest repository for environmental E. coli strains in America.EcoliWiki page
E. coli student portalE. coli Student PortalEcoliWiki page
ECCEE. coli Cell Envelope ProteinsEcoliWiki page
EchoBASECurated experimental and bioinformatic information about E. coli genes and gene productsEcoliWiki page
EciDFor exploring the sizeable amount of protein interaction-related data available for Escherichia coliEcoliWiki page
EcoCycComprehensive database of E. coli molecular componentsEcoliWiki page
ECODABEscherichia coli O-antigen DatabaseEcoliWiki page
EcoGeneEcoGene, comprehensive data resource for E. coliEcoliWiki page
EcoliWikiWiki-based community annotation for ''E. coli'' K-12, as part of [http://PortEco.org PortEco]EcoliWiki page
EcoProDBIntegrates protein information identified on 2-D gels along with other resources.EcoliWiki page
ECORA reference collection of E. coli strains found in natureEcoliWiki page
EcoSalReview articles on topics related to E. coli and SalmonellaEcoliWiki page
EducauseEducauseEcoliWiki page
EhrmannEcoliWiki page
eNetGene function prediction and annotation of ''Escherichia coli'' K12 proteins using physical protein-protein interactions, genomic context methods and machine learning algorithmsEcoliWiki page
Ensembl ComparaA genome databases for vertebrates and other eukaryotic speciesEcoliWiki page
ERICEnteropathogen Resource Integration CenterEcoliWiki page
Escherichia coli K-12 ProteinsCharacterize functions of unknown Escherichia coli K-12 proteins.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 dbCompiles all complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences in aligment format.EcoliWiki page
ExPASy proteomics serverAnalysis of protein sequences and structures.EcoliWiki page
Faculty of 1000Highlights and reviews of papers in the biological sciences recommended as interesting by members of the Faculty of 1000.EcoliWiki page
FAMSBASEProtein structure models by homology modelingEcoliWiki page
Felix d Herelle Reference Center for bacterial virusesFélix d'Hérelle Reference Center for bacterial viruses of the Université LavalEcoliWiki page
Fellowship for the Interpretation of Genomes (FIG)Analysis of subsystems across multiple genomesEcoliWiki page
FlyBaseGenetic and molecular data for D. melanogaster and other Drosophila species.EcoliWiki page
FusionDBProkaryotic gene fusion events EcoliWiki page
GenExpDB''E. coli'' Gene Expression DatabaseEcoliWiki page
Gene Expression Omnibus (GEO)NCBI archive of expression dataEcoliWiki page
Gene Ontology (GO)Provides a controlled vocabulary to describe gene and gene product attributes in any organism.EcoliWiki page
GenoBasePublic 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 genomesEcoliWiki page
Genomic tRNA databaseGenomic tRNA database contains tRNA gene predictions made by the program tRNAscan-SE.EcoliWiki page
GenProtECFunctions encoded by the Escherichia coli K-12EcoliWiki page
GIRCMicrobial Gene ProductsEcoliWiki page
GMODAn open source project for creating and managing genome-scale biological databases. See the [http://gmod.org/wiki/Overview project overview] for more.EcoliWiki page
GOLD:Genomes Online DatabaseInformation about genome and metagenome sequencing projects, and their associated metadata.EcoliWiki page
GONUTSGene Ontology Normal Usage Tracking System (GONUTS) Community curation of usage notes for GO and GO annotations for genes EcoliWiki page
GTOPData analyses of proteins, sequence homology analyses, and three-dimensional structures of proteins.EcoliWiki page
HHMI Science Education AllianceHHMI Science Education AllianceEcoliWiki page
High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP)UniProt/ExPASY component EcoliWiki page
HOGENOMDatabase of Complete Genome Homologous Genes FamiliesEcoliWiki page
Information Hyperlinked Over Proteins (IHOP)A way of accessing millions of PubMed abstracts.EcoliWiki page
InParanoidEukaryotic Ortholog GroupsEcoliWiki page
IntActDatabase of protein-protein interactions derived from literature curation or direct user submissions. EcoliWiki page
Integrated Microbial GenomesJoint Genome Intstitute's Microbial GenomesEcoliWiki page
IntEnzIntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature.EcoliWiki page
International Committee on Taxonomy of Viruses (ICTVdB)Virus databaseEcoliWiki page
INternational RIce Information SystemInternational Rice Information System "A Platform for Meta-Analysis of Rice Crop Data"EcoliWiki page
InteroperationEcoliWiki page
InterProEcoliWiki page
IsfinderList of insertion sequences isolated from eubacteria and archae.EcoliWiki page
JGI - Undergraduate Research in Microbial Genome AnnotationDOE Joint Genome Institute’s Education ProgramEcoliWiki page
JGI Genome PortalJoint Genome Institute Genome Portal EcoliWiki page
Kyoto Encyclopedia of Genes and Genomes (KEGG)Encyclopedia of Genes, Genomes, and PathwaysEcoliWiki page
Many Microbe Microarrays Database (M3D)Affymetrix data for ''E. coli'' and other bacteriaEcoliWiki page
Membrane Protein Data Bank (MPDB)A database for membrane proteinsEcoliWiki page
MEROPSResource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. EcoliWiki page
MetaBaseA Database of Databases EcoliWiki page
Microbes OnlineEcoliWiki page
Microbe LibraryMicrobe LibraryEcoliWiki page
Microbe ProjectA Portal to U.S. Federal efforts in microbial research.EcoliWiki page
Microbial Signal Transduction (MiST)Signal transduction proteins from bacteria and archaea.EcoliWiki page
Microbiology On-lineMicrobiology On-LineEcoliWiki page
ModBase3-dimensional protein models from comparative modelingEcoliWiki page
Molecular Life Sciences Concept InventoryMolecular Life Sciences Concept InventoryEcoliWiki page
Mouse Genome Informatics (MGI)Integrated access to data on the genetics, genomics and biology of the laboratory mouseEcoliWiki page
MTBbaseEcoliWiki page
Mycobacteriophage DatabaseData and tools related to phages that infect the Mycobacteria. EcoliWiki page
MycozomeA database for the comparative studies of fungal genomes.EcoliWiki page
National Center for Case Study Teaching in ScienceEcoliWiki page
National Food Safety %26 Toxicology CenterInformation about E. coli food pathogensEcoliWiki page
National Science Digital LibraryNational Science Digital LibraryEcoliWiki page
NCBINational Center for Biotechnology InformationEcoliWiki page
NCBI Short Read ArchiveRepository of reads from high-throughput sequencing at NCBIEcoliWiki page
Neurospora at MIPSDatabase for the molecular structure and functional network of Neurospora crassa.EcoliWiki page
NHGRINational Human Genome Reasearch InstituteEcoliWiki page
NONCODEnoncoding RNA databaseEcoliWiki page
Noncoding RNA databaseA 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
NSF Vision and ChangeNSF & AAAS Vision and Change in Undergraduate Biology EducationEcoliWiki page
Online Bioinformatics Resources Collection (OBRC)Online Bioinformatics Resources CollectionEcoliWiki page
OpenWetWareWiki-based collection of lab websites, with information on materials, protocols, and courses.EcoliWiki page
Open BiosystemsA service to distribute biological resources, especially genome scale setsEcoliWiki page
ORENZAdatabase of ORphan ENZyme ActivitiesEcoliWiki page
Orientations of Proteins in Membranes (OPM)Orientations of Proteins in MembranesEcoliWiki page
PantherPANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System EcoliWiki page
PathguideA list of tools and datasets of biological pathways/networks.EcoliWiki page
Pathogen PortalRepository linking 8 Bioinformatics Resource Centers sponsored by the National Institute of Allergy and Infectious Disease (NIAID).EcoliWiki page
PATRICPATRIC, the PathoSystems Resource Integration Center, is a multi-faceted bioinformatic website containing genomic and associated information on the eight important human pathogens: Brucella, Coxiella, Rickettsia, Caliciviridae, Coronaviruses, Hepatitis A and E viruses, and Lyssaviruses. EcoliWiki page
PECProfiling ''E. coli'' Chromosome PEC focuses on gene functionEcoliWiki page
Pedro%27s molecular biology toolsEcoliWiki page
PGDCollate biological and genomic data for all bacterial plasmids for interrogation of both meta- and genomic data.EcoliWiki page
PhantomePhAnToMe (Phage Annotation Tools and Methods) is a platform that we are currently developing for phage genome annotations.EcoliWiki page
PhenomicDBa multi-species genotype/phenotype databaseEcoliWiki page
phiSITEDatabase of Gene Regulation in BacteriophagesEcoliWiki page
PHOSIDAPhosida - Phosphorylation Site DatabaseEcoliWiki page
Phylogenomic Display of Bacterial Genes (Phydbac)Phylogenomic Display of Bacterial Genes (Phydbac)EcoliWiki page
PhylomeDBA database for genome-wide collections of gene phylogenies.EcoliWiki page
PIRSFPIRSF (Protein information Resource)EcoliWiki page
Pittsburgh Bacteriophage InstituteSequences of bacteriophages determined in at Pitt (as well as sequences of other notable phages), publications, and much more.EcoliWiki page
plant microRNAEcoliWiki page
Plant OrganellesEcoliWiki page
Plasmodium falciparium DatabaseMalaria Database Our goal is to make the genome sequence of organisms rapidly and broadly available to the scientific community. The genome sequencing community recently adopted a statement of principles for the distribution and use of large-scale sequencing data (http://www.genome.gov/page.cfm?pageID=10506376).EcoliWiki page
plasmodium falciparumThis Database is used for Toxoplasma Genomics ResourcesEcoliWiki page
PMTGE. coli short DNA repeats, super integrons, ABC transporters, and genomic toxicologyEcoliWiki page
PortEcoA next-generation resource for knowledge and data about the biology of Escherichia coli laboratory strains, its bacteriophages, plasmids and mobile genetic elements.EcoliWiki page
PortEco/expression.porteco.orgGene Expression analysis component of the [[PortEco]] projectEcoliWiki page
PQSPredicted quaternary structure for structures deposited at the PDBEcoliWiki page
Princeton Protein Orthology Database (P-POD)Princeton Ortholog DatabaseEcoliWiki page
ProDOMProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.EcoliWiki page
PROSITEDatabase of protein domains, families and functional sitesEcoliWiki page
ProtComA 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 OntologyEcoliWiki page
Protein Information Resource (PIR)Protein sequences and functional informationEcoliWiki page
Protein Link Explorer (PLEX)Protein Link ExplorerEcoliWiki page
ProteopediaWiki based information about protein structures EcoliWiki page
ProThermA collection of numerical data of thermodynamic parameters for wild type and mutant proteins.EcoliWiki page
Pseudomonas Genome DatabasePseudomonas aeruginosa genome informationEcoliWiki page
PubMedSearch 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
ReactomeOpen-source, curated resource of core pathways and reactions in human biology. EcoliWiki page
REFOLDDatabase of refolding protocols for protein purificationEcoliWiki page
RefSeqEcoliWiki page
RegTransBaseA database of regulatory sequences and interactions in a wide range of prokaryotic genomesEcoliWiki page
RegulonDBRegulonDB provides information on operon organization and regulation in ''E. coli.''EcoliWiki page
RFamRFam - RNA familiesEcoliWiki page
Ribosomal Protein Gene Database (RPG)Ribosomal protein gene orthologs from different prokaryotes and eukaryotesEcoliWiki page
RNAmodsComprehensive listing of post-transcriptionally modified nucleosides from RNAEcoliWiki page
RoundUp - Orthology DatabaseA database of orthologs and corresponding evolutionary distances.EcoliWiki page
Science.govScience.govEcoliWiki page
ScientistSolutionsThe International Life Science ForumEcoliWiki page
SCORA database that provides understanding of RNA motif structure, function, tertiary interactions and their relationships.EcoliWiki page
SDSU Microbial Informatics GroupEcoliWiki page
Sequence OntologySequencing annotation data.EcoliWiki page
SGDComprehensive data resource for ''S. cerevisiae'' (baker's yeast) EcoliWiki page
SHIGENShared Information of Genetic ResourcesEcoliWiki page
SilvaComprehensive ribosomal RNA database EcoliWiki page
SMARTSMART (a Simple Modular Architecture Research Tool)EcoliWiki page
Society for College Science TeachersSociety for College Science TeachersEcoliWiki page
Society for General MicrobiologySociety for General MicrobiologyEcoliWiki page
sRNAMapSmall noncoding RNA MapEcoliWiki page
Stanford MicroArray DatabaseThe 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
StringEcoliWiki page
Structural Classification of Proteins (SCOP)Structural Classification of ProteinsEcoliWiki page
Structural Proteomics Experimental Database (SPEX)EcoliWiki page
SubtiListDatabase that analyzes the genome of Bacillus subtilis.EcoliWiki page
SuperfamilySuperfamilyEcoliWiki page
SwedCAD DatabaseA database of annotated high-mass accuracy MS/MS spectra of tryptic peptidesEcoliWiki page
Swiss-modelProtein structure modeling tool and repository of modelsEcoliWiki page
T4-like genome databaseGenome information about T4-like bacteriophageEcoliWiki page
TBDBAn integrated platform for tuberculosis researchEcoliWiki page
TDR Targets DatabaseSearchable database for drug targets for tropical diseasesEcoliWiki page
The Arabidopsis Information Resource (TAIR)TAIR is the model organism database for Arabidopsis thaliana.EcoliWiki page
The Bacteriophage Ecology GroupThe Bacteriophage Ecology Group - Home of Phage Ecology and Phage Evolutionary BiologyEcoliWiki page
The Comprehensive Antibiotic Resistance DatabaseA bioinformatic database of resistance genes, their products and associated phenotypes.EcoliWiki page
The Genomics Education National Initiative (GENI)Developing Genomics for EducationEcoliWiki page
TIGRFAMSTIGRFAMSEcoliWiki page
tmRNA websiteSearchable list of tmRNAEcoliWiki page
TOPSANCommunity annotation of protein structures determined by structural genomics centersEcoliWiki page
ToxoplasmaThis website contains toxoplasma genomics databases.EcoliWiki page
TreeFamTree families databaseEcoliWiki page
TubercuListTubercuList provides a complete dataset of DNA and protein sequences derived from the strain ''M. tuberculosis'' H37Rv.EcoliWiki page
UniProtComprehensive protein resourceEcoliWiki page
VectorDBInformation about cloning vectorsEcoliWiki page
ViralZoneViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries. EcoliWiki page
Web of ScienceSearch tools for scientific literature (subscription required)EcoliWiki page
wFleaBaseThis database has been providing genome information for researchers about the organism Daphnia pulex, this is a fresh-water crustacean of world distribution, widely used in research on ecology, environmental toxicology.EcoliWiki page
WikiPathwaysWikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. EcoliWiki page
WikiProteinsEcoliWiki page
Workforce Development for Teachers and ScientistsWorkforce Development for Teachers and Scientists (WDTS)EcoliWiki page
WormBaseC. elegans genome informationEcoliWiki page
XanthusBaseMyxococcus xanthus genome informationEcoliWiki page
Zebrafish Information Network (ZFIN)Zebrafish Information Network (ZFIN)EcoliWiki page

See Also

Category:Bioinformatics Tools

Subcategories

This category has the following 22 subcategories, out of 22 total.

Pages in category "Databases"

The following 200 pages are in this category, out of 238 total.

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