Resources on the Internet

Here we historically provided links to research resources beyond our lab. Many have become invalid over the years; 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
Microarray and Functional Genomics


On the UW-Madison campus

E. coli related resources

General E. coli information

Pathogenic E. coli

Databases and data collections (mostly E. coli K-12)

  • IECA the International E. coli Alliance's database portal
  • EcoGene the comprehensive data resource structural and functional annotation of E. coli K-12
  • CGSC the Coli Genetic Stock Center at Yale University
  • EcoCyc the bioinformatics database describing the genome and biochemical machinery of E. coli K-12
  • PortEco data resource for the bacterial model organism, Escherichia coli (formerly EcoliHub)
  • GenoBase functional genomic analysis of E. coli in Japan
  • EchoBASE an integrated post-genomic database for E. coli
  • ECDC the E. coli Database Collection
  • PrFEcT an online open-access protein function and verification database
  • RegulonDB E. coli K-12 transcriptional regulatory network
  • transportDB predicted cytoplasmic membrane transport proteins
  • PEC profiling of the E. coli chromosome
  • E. coli | Zhang Lab Genome-wide protein structure & function modeling
  • ECCE the E. coli cell envelope protein data collection
  • proteases of E. coli
  • E. coli transcription factor binding sites
  • repeated sequences short repeated palindromes in enterobacteria
  • ECODAB Escherichia coli O-antigen Database
  • ECOR Strains the Escherichia coli Reference Collection of natural isolates
  • LTEE the E. coli Long-term Experimental Evolution project
  • ** GenProtEc, an E. coli genome and proteome database at MBL, has been retired **

The lighter side of E. coli

 

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 1000 completed or ongoing sequencing projects for strains of E. coli alone. In addition to a few enterobacterial projects, here are links to major microbial sequencing centers, multi-organism databases, and related resources.

  • salmonella.org
  • AToL: Enterobacteriaceae project to sequence Type strains of the family Enterobacteriaceae
  • GOLD the Genomes OnLine Database
  • Microbial Genome Projects Genome Information Research Center, Osaka Univ
  • Bacterial Genomes Wellcome Trust Sanger Institute
  • Genomes: Microorganisms The Genome Institute, Washington University
  • PATRIC Pathosystems Resource Integration Center, a Bacterial Bioinformatics Resource Center
  • xBASE a comprehensive resource for comparative bacterial genomics
  • GenoList an integrated environment for the analysis of microbial genomes
  • JGI Genome Portal DOE's Joint Genome Institute
  • Microbial Genomes at NCBI public data from prokaryotic genome sequencing projects
  • BioCyc pathway/genome databases (including EcoCyc)
  • KEGG Kyoto Encyclopedia of Genes and Genomes
  • MicrobesOnline an integrated portal for comparative and functional genomics
  • Genome Atlas Database from Technical University of Denmark's Center for Biological Sequence Analysis
  • BacMap interactive Bacterial Genome Atlas
  • UCSC Microbial Genome Browser a microbe-specific version of the popular visualization tool
  • ASAP a systematic annotation package for community analysis of genomes
  • IMG DOE's Integrated Microbial Genomes ** account needed as of January 7, 2014 **
  • ** JCVI's Comprehensive Microbial Resource (CMR) is no longer supported and has been taken offline **

Microarray and Functional Genomics

  • MIAME Minimal Information About Microarray Experiment
  • SMD Stanford Microarray Database
  • ArrayExpress a database of functional genomics experiments

 


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