Resources on the Internet

Here we historically provided links to research resources beyond our lab. Many have become invalid over the years, succumbing to bit-rot; broken links are periodically fixed or deleted, but no wholesale update is anticipated. We are open to suggestions for additional links.

On the UW-Madison campus
E. coli related resources
Other Enterobacterial genome projects


On the UW-Madison Campus

E. coli Related Resources

General E. coli Information

Pathogenic E. coli

  • Pathogenic E. coli chapter from Todar's Online Textbook of Bacteriology
  • E. coli | CDC general information from the Centers for Disease Control and Prevention
  • E. coli | FoodSafety.gov general information from the U.S. Food & Drug Administration
  • The FDA's Foodborne Pathogenic Microorganisms and Natural Toxins Handbook,
    aka The Bad Bug Book (Second Edition)
  • E. coli Reference Center at Penn State: largest repository for E. coli strains in America
  • EcMLST a multilocus sequence typing (MLST) database for pathogenic E. coli
  • PAIDB the Pathogenicity Island Database: pathogenicity islands and antimicrobial resistance islands

Databases and Data Collections (mostly E. coli K-12)

  • EcoCyc the bioinformatics database describing the genome and biochemical machinery of E. coli K-12
  • CGSC the Coli Genetic Stock Center at Yale University
  • E. coli Strain NBRP Japanese National BioResource Project for strains, clones, cloning vectors and more
  • EcoliWiki a subsystem for community annotation of E. coli, its phages, plasmids, and mobile genetic elements.
  • EchoBASE an integrated post-genomic database for E. coli
  • RegulonDB E. coli K-12 transcriptional regulatory network
  • transportDB predicted cytoplasmic membrane transport proteins
  • GenExpDB the E. coli Gene Expression Database at Oklahoma State University
  • CCDB the CyberCell database: quantitative genomic, proteomic, and metabolomic data on E. coli
  • ECMDB the E. coli Metabolome Database
  • Bacteriome.org a database of E. coli protein-protein interactions
  • PEC profiling of the E. coli chromosome
  • EcoProDB the E. coli protein database, integrating 2-D gel data with other resources
  • E. coli | Zhang Lab genome-wide protein structure & function modeling
  • E. coli Proteases and their cellular localisation
  • ECODAB the Escherichia coli O-antigen Database
  • LTEE the E. coli Long-Term Evolution Experiment, observing bacterial evolution in action since 1988

E. coli in the Arts and Beyond

 

Other Enterobacterial genome projects (aka the Deluge)

Keeping track of the multitude of other genome projects has become a Sisyphean task; there are well over 180,000 completed or ongoing sequencing projects for strains of E. coli alone. Here are links to major microbial sequencing centers, multi-organism databases, and related resources.

  • SalmoNet 2.0 An integrated multi-layered network of Salmonella
  • Microbial Genomes at NCBI public data from prokaryotic genome sequencing projects
  • Bacterial Genomes bacteria sequenced at the Wellcome Sanger Institute
  • NIH Human Microbiome Project
  • GOLD the Genomes OnLine Database
  • IMG/M DOE's Integrated Microbial Genomes & Microbiomes
  • JGI Genome Portal DOE's Joint Genome Institute
  • BV-BRC the Bacterial and Viral Bioinformatics Resource Center
  • ATCC Genome Portal a comprehensive collection of microbial genomics reference data
  • EnteroBase, a resource for analyzing and visualizing genomic variation within enteric bacteria
    includes databases for Escherichia/Shigella, Salmonella, Mycobacterium, Streptococcus, Clostridioides, Vibrio, Yersinia, Helicobacter, & Moraxella
  • BioCyc Pathway/Genome Databases; EcoCyc is freely available, but access to the remaining BioCyc databases (over 20,000 organisms) requires a paid subscription
  • KEGG the Kyoto Encyclopedia of Genes and Genomes; part of GenomeNet, a Japanese network of database and computational services for genome research
  • MiMeDB the Microbial Metabolites Database, containing detailed information about small molecule metabolites found in the human microbiome
  • MicrobesOnline an integrated portal for comparative and functional genomics
  • BacMap an Interactive Atlas for Exploring Bacterial Genomes
  • UCSC Microbial Genome Browser a microbe-specific version of the popular visualization tool
  • ASAP a systematic annotation package for community analysis of genomes
  • DEG: Database of Essential Genes from the Centre of Bioinformatics, Tianjin University

Prokaryote (& Virus) Taxonomy

 


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