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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
- E. coli Strain NBRP Japanese National BioResource Project for strains, clones, cloning vectors and more
- 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
- RegulonDB E. coli K-12 transcriptional regulatory network
- transportDB predicted cytoplasmic membrane transport proteins
- PEC profiling of the E. coli chromosome
- ECMDB the Escherichia coli Metabolome Database: the genome and metabolome of E. coli K-12
- PrFEcT-Predict a database of computational resources for multiple proteomes
- EcoProDB the E. coli protein database, integrating 2-D gel data with other resources
- 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; EcoCyc and other organism entry pages:
- 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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