This list is a collection of biological online databases. We provide these resources in order to promote the development of an integrated view of gene regulation as a complementation of the information contained in RegulonDB. The categories, in which the databases are grouped, are approximate because they contain multiple data types, so they can belong to multiple categories.

DATABASE	LINKS	DESCRIPTION
KEGG	http://www.genome.ad.jp/kegg/	This Website is a complete computer representation of the cell, the organism, and the biosphere, which will enable computational prediction of higher-level complexity of cellular processes and organism behaviors from genomic and molecular information.
BioCyc	http://biocyc.org/	BioCyc is a collection of 371 Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism.
SubtiList	http://genolist.pasteur.fr/SubtiList/	This Website is dedicated to the analysis of the genome of Bacillus subtilis. It provides a complete dataset of DNA and protein sequences.
SwissRegulon database	http://www.swissregulon.unibas.ch	This is a database that contains genome-wide annotations of regulatory sites.
PEC	http://www.shigen.nig.ac.jp/ecoli/pec/index.jsp	The Profiling of the Escherichia coli chromosome (PEC) database has been constructed to compile any relevant information that could help to characterize the E. coli genome, especially with respect to discovering the function of each gene.
CMR	http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi	The Comprehensive Microbial Resource (CMR) is a free Website used to display information regarding all the publicly available and complete prokaryotic genomes.
Microbe Project	http://www.microbeproject.gov/	A Portal to U.S. Federal Efforts in Microbial Research.
(coliBASE)	http://www.xbase.ac.uk/colibase/	This site is a database for comparative genome analysis of Enterobactericaiae Chaudhuri et al., 2006. Database for E. coli, Salmonella and Shigella. Comparative genome analysis.
RefSeq	http://www.ncbi.nlm.nih.gov/RefSeq/	The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.
ASAP	https://asap.ahabs.wisc.edu/asap/ASAP1.htm	A Systematic Annotation Package to store, update and distribute genome sequence and gene expression data.
CGSC: Coli Genetics Stock Center	http://cgsc.biology.yale.edu/	This ste contains information about genotypes, reference information for the strains in the CGSC collection, names, synonyms, properties and map position for genes, gene product information, as well as information on specific mutations and references to primary literature.
E. coli Genome Project at UW-Madison	http://www.genome.wisc.edu/	Genomic sequence data of various organisms and their annotation. It has a knockout of every gene, a clone of every ORF and an extensive gene expression dataset under a variety of physiological conditions.
E. coli Reference Center	http://ecoli.cas.psu.edu/	This database is the largest repository for E. coli strains in America.
ECDC	http://www.uni-giessen.de/ecoli/ECDC/ecdc.htm	This site contains information regarding the entire E.coli K12 chromosome.
Fellowship for the Interpretation of Genomes (FIG)	http://www.theseed.org/wiki/Main_Page	Analysis of subsystems across multiple genomes.
GIRC	http://genome.bio.titech.ac.jp/bacteria/	This site provides a variety of genome links.
GMOD	http://gmod.org/wiki/Main_Page	GMOD is the Generic Model Organism Database project, a collection of open source software tools for creating and managing genome-scale biological databases.
Integrated Microbial Genomes	http://img.jgi.doe.gov/cgi-bin/pub/main.cgi	IMG serves as a community resource for comparative analysis and annotation of all publicly available genomes of the three domains of life in a uniquely integrated context.
EnteriX	http://enterix.cbcb.umd.edu/	This site allows comparative views of a reference genome (E. coli K-12 or O157:H7, S. typhimurium LT2, S. typhi CT18, S. paratyphi A, K. pneumoniae, E. sakazakii, C. koseri, Y. pestis, P. aeruginosa PAO1 or S. enteritidis str. P125109) with sequences from several related bacteria using two different visualization tools. The Enteric server offers large-scale views of pairwise alignments, with point-and-click capabilities to retrieve related gene and alignment information. The Menteric tool displays nucleotide-level multiple alignments of the bacterial sequences, along with regulatory site annotations which the user interested in conservation and functional studies may want to explore further.
EcoCyc	http://ecocyc.org/	EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.

TRANSCRIPTION FACTORS / GENE REGULATION

DATABASE	LINKS	DESCRIPTION
BiGRe	http://www.bigre.ulb.ac.be/	Genome and Network Bioinformatics
RegTransBase	http://regtransbase.lbl.gov.	Database of regulatory interactions based on literature and an expertly curated database of transcription factor binding sites.
OrthoMCL-DB	http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi	Ortholog Grouping of Protein Sequences of Multiple Genomes.
ProDOM	http://prodom.prabi.fr/prodom/current/html/home.php	ProDom is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases.
RSA Tools	(http://embnet.ccg.unam.mx/rsat/)	Regulatory Sequences Analysis Tools offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA sequences.
RoundUp - Orthology Database	http://roundup.hms.harvard.edu/	Roundup is a large-scale database of orthology, covering over 220 publicly available genomes.
Phylogenomic Display of Bacterial Genes (Phydbac)	http://igs-server.cnrs-mrs.fr/phydbac/	Phydbac is a Web interactive tool that displays phylogenomic profiles of bacterial protein sequences. It also provides a way to identify, in a given organism, the proteins that have the most similar sequence conservation profiles to a query protein. The analysis of the annotation of those phylogenomic neighbors may help to generate hypothetical functions for querying proteins.
PredictRegulon	http://www.cdfd.org.in/servicespages/bioinformatics.html	A Web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes.
Tractor_DB	http://www.ccg.unam.mx/Computational_Genomics/tractorDB/	Tractor_DB (v.2.0) contains a collection of computationally predicted Transcription Factors' binding sites in gamma-proteobacterial genomes. These data should aid researchers in the design of microarray experiments and the interpretation of their results. They should also facilitate studies of Comparative Genomics of the regulatory networks of this group of organisms.
ODB	http://www.genome.sk.ritsumei.ac.jp/odb/	Operon database aims to collect known operons in multiple species and offers a system to predict operons by user definitions. All the known operons are derived from literature and publicly available databases, including operon information.
MycoperonDB	http://cdfd.org.in/mycoperondb/home.html	MycoperonDB is setup to provide operon and trancriptional unit information of different mycobacterial species at one place. It is a database of computationaly predicted operons and transcriptional units of Mycobacteria.
PromEC	http://margalit.huji.ac.il/promec/	This site contains a collection of E. coli promoters with experimentally-identified transcriptional start sites.
AraC-XylS	http://www.eez.csic.es/arac-xyls/	This site is a family of positive transcriptional regulators in bacteria and a Protein Data Base
Colibri	http://genolist.pasteur.fr/Colibri/	Complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12.
CoryneRegNet 4.0	http://www.coryneregnet.de/	A reference database for corynebacterial gene regulatory networks, Transcription Factors and Regulatory Networks.
DBD	http://www.transcriptionfactor.org/	Transcription Factor prediction database.
DBTBS	http://dbtbs.hgc.jp/	Bacillus subtilis promoters and Transcription Factors, regulated Operons and Motif conservation.
EchoBASE	http://www.ecoli-york.org/	Post-genomic studies of Escherichia coli.
EcoGene	http://ecogene.org/	Sequence and literature data on E. coli genes and protein sequences and Function.
EcoTF	http://ecotfs.lanl.gov/index1.shtml	Transcription Factors and signals that control their activity.
JASPAR	http://jaspar.cgb.ki.se/	PSSMs for Transcription Factor DNA-binding sites. The high-quality Transcription Factor binding profile database.
JGI Microbial Genomics	http://genome.jgi-psf.org/mic_home.html	The Joint Genome Institute has released prokaryotic microbial sites for sequence files, Blast and view annotations.
Escherichia coli transcription factor binding sites (TFBS)	http://bayesweb.wadsworth.org/binding_sites/index.html	This site presents Transcription Factor binding site predictions in the E. coli genome made by cross-species comparison (i.e. phylogenetic footprinting).
TRACTOR db	http://www.ccg.unam.mx/Computational_Genomics/tractorDB/	Tractor_DB (v.2.0) contains a collection of computationally predicted Transcription Factors' binding sites in gamma-proteobacterial genomes. These data should aid researchers in the design of microarray experiments and the interpretation of their results. They should also facilitate studies of Comparative Genomics of the regulatory networks of this group of organisms.
TFinDit Transcription Factor-DNA Interaction Data Depository	http://bioinfozen.uncc.edu/tfindit/	TFinDit is a database and web service for structural bioinformatics studies of transcription factor (TF)-DNA interactions. Various datasets can be generated based on one or more search options specified by users.
CollectTF	http://collectf.umbc.edu/home/greet/	CollecTF is a database of transcription factor binding sites (TFBS) in the Bacteria domain.

DATABASE	LINKS	DESCRIPTION
AlignACE	http://arep.med.harvard.edu/ecoli_matrices/	Sequence-specific DNA-binding proteins perform a variety of roles in the cell, including transcriptional regulation.
MPDB (Membrane Protein Data Bank)	http://www.mpdb.tcd.ie/	Database that contains structural information on integral, peripheral and anchored membrane proteins and peptides.
PHOSIDA	http://www.phosida.de/	PHOSIDA (phosphorylation site database): management, structural and evolutionary research, and prediction of phosphosites.
PRIDE	http://www.ebi.ac.uk/pride/	PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data.
SCOP	http://scop.mrc-lmb.cam.ac.uk/scop/	This site shows Structural Classification of Proteins.
STRING	http://string.embl.de/	This site shows known and predicted protein-protein associations integrated and transferred across organisms.
Structural Proteomics Experimental Database (SPEX)	http://euler.bri.nrc.ca/brimsg/bsgi.html	Bacterial Structural Genomics Initiative (BSGI). Structural Proteomics Experimental Database. This database determines thousands of protein structures by developing high-throughput techniques for all steps of the experimental structure determination pipeline.
ProTISA	http://mech.ctb.pku.edu.cn/protisa/	Translation Initiation Site Annotation in prokaryotic genomes
BRENDA	http://www.brenda-enzymes.info/	This site is the main collection of enzyme functional data available to the scientific community.
CCDB	http://redpoll.pharmacy.ualberta.ca/CCDB	CyberCell Database is collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data.
COGs	http://www.ncbi.nlm.nih.gov/COG/old/	COGs contains a phylogenetic classification of proteins encoded in complete genomes.
Conserved Domain Database (CDD)	http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml	CDD is a collection of multiple sequence alignments for ancient domains and full-length proteins.
DPInteract	http://arep.med.harvard.edu/dpinteract/	Binding sites for E. coli DNA-binding proteins.
ECCE	http://www.cf.ac.uk/biosi/staffinfo/ehrmann/tools/ecce/ecce.htm	Cell envelope protein data Collection
Ehrmann	http://www.cf.ac.uk/biosi/staffinfo/ehrmann/	Protein Biogenesis and Function are studied with a particular interest in integral membrane proteins. We are addressing general biological questions, such as protein folding and degradation, or the mechanism of active transport.
ExPASy proteomics server	http://www.expasy.org	The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures, as well as 2-D PAGE.
Gene Ontology (GO)	http://geneontology.org/	The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
GenProtEC	http://genprotec.mbl.edu/	E. coli K12 genome and proteome database.
GTOP	http://spock.genes.nig.ac.jp/%7Egenome/gtop.html	Genomes TO Protein structures and functions
High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP)	http://ca.expasy.org/sprot/hamap/	Proteins that are part of well-conserved families or subfamilies.
Information Hyperlinked Over Proteins (IHOP)	http://www.ihop-net.org/UniPub/iHOP/	Information hyperlinked over proteins
IntAct	http://www.ebi.ac.uk/intact/site/index.jsf	IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature, curation or direct user submissions and are freely available.
InterPro	http://www.ebi.ac.uk/interpro/	Protein families, domains, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences.
PDIdb Protein-DNA Interface Database	http://melolab.org/pdidb/web/content/home	PDIdb (Protein-DNA Interface database) is a repository containing relevant structural information of Protein-DNA complexes solved by X-Ray cristallography and available at the Protein Data Bank (PDB). The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels (Class, Type and Subtype).
footprintDB	http://floresta.eead.csic.es/footprintdb/index.php	footprintDB is a database with 2905 unique DNA-binding proteins (mostly transcription factors, TFs) and 4001 Position Weight Matrices (PWMs) extracted from the literature and other repositories.
PFAM	http://pfam.xfam.org/	The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
Superfamily DB	http://supfam.org/SUPERFAMILY/	SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.

RNA

DATABASE	LINKS	DESCRIPTION
RFam	http://www.sanger.ac.uk/Software/Rfam/	RNA families database of alignments and covariance models.
tmRNA website	http://www.indiana.edu/%7Etmrna/	The bacterial tmRNA is so-named for its dual tRNA-like and mRNA-like nature.
5S rRNA Database	http://biobases.ibch.poznan.pl/5SData/	This site contains information on nucleotide sequences of 5S rRNAs and their genes.
Genomic tRNA-Database	http://lowelab.ucsc.edu/GtRNAdb/	This database contains tRNA identifications made by the program tRNAscan-SE on complete or nearly complete genomes.
IntEnz	http://www.ebi.ac.uk/intenz/	Integrated relational Enzyme database is a freely available resource focused on enzyme nomenclature.
mRNA abundance data.	http://arep.med.harvard.edu/mrnadata/expression.html	mRNA abundance data from the George M. Church lab.

BIOLOGICAL PATHWAYS AND NETWORKS

DATABASE	LINKS	DESCRIPTION
MIST (Microbial Signal Transduction)	http://genomics.ornl.gov/mist/	This site contains the signal transduction proteins of 707 complete bacterial and archaeal organisms.
SYSTOMONAS	http://systomonas.tu-bs.de/	SYSTOMONAS is a comprehensive database about molecular networks in pseudomonas with focus on Pseudomonas aeruginosa and based on PRODORIC, as well as KEGG, and is closely connected to BRENDA.
PathBLAST	http://www.pathblast.org/	PathBLAST is a network alignment and search tool for comparing protein interaction networks across species to identify protein pathways and complexes that have been conserved by evolution.
WikiPathways	http://www.wikipathways.org/index.php/WikiPathways	This site is an open, public platform dedicated to the curation of biological pathways by and for the scientific community.
EcoCyc	http://ecocyc.org/	E. coli K12 genes, pathways, transporters, and gene regulation.
MetaCyc	http://metacyc.org/	MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1,100 pathways from more than 1,500 different organisms.
ecoli.aist-nara.ac.jp	http://ecoli.aist-nara.ac.jp/index.html	This site provides information obtained in the "Functional Genomic Analysis of E. coli in Japan", in collaboration with the international E. coli consortia.
GeneNet	http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/	GeneNet is a database on gene network components, as well as database on structure and functional organisation of gene networks.
GenePattern	http://www.broad.mit.edu/cancer/software/genepattern/	This site combines a powerful scientific workflow platform with more than 90 computational and visualization tools for the analysis of genomic data.
GeNet - Gene Networks Database	http://www.bionet.nsc.ru/meeting/bgrs/thesis/17/index.html	GeNet is a hypertext database. The concept of genetic networks forms a basis for information structuring in this database - each of the thus far characterized genes is considered as a node of a genetic network, while the links between nodes represent the interactions of genes or their products.

GENE EXPRESSION

DATABASE	LINKS	DESCRIPTION
COLOMBOS	http://colombos.net/	Colombos stands for 'Collection Of Microarrays for Bacterial OrganismS'. It is a web based portal for exploring and analyzing comprehensive organism-specific cross-platform expression compendia of bacterial organisms.
PRODORIC	http://prodoric.tu-bs.de/	Prokaryotic database of gene regulation networks.
Stanford Microarray DB	http://genome-www5.stanford.edu/	SMD, the Stanford Microarray Database, stores raw and normalized data from microarray experiments and provides data retrieval, analysis and visualization.
ArrayExpress	http://www.ebi.ac.uk/arrayexpress/	Repository for transcriptomics data.
Many Microbe Microarrays Database (M3D)	http://m3d.bu.edu/cgi-bin/web/array/index.pl?section=home	This database is a resource for analyzing and retrieving gene expression data for microbes.
CIBEX	http://cibex.nig.ac.jp	Center for informational Biology gene Expression database. Microarray data
E. coli GenExpD. This is the University of Oklahoma's E. coli Gene Expression Database	http://chase.ou.edu/oubcf/	E. coli Gene Expression Database is the University of Oklahoma's E. coli Gene Expression Database.
E. coli Entry Point. Berkeley E. coli Microarray Database	http://coli.berkeley.edu/ecoli/	E. coli Functional annotation. Connection to microarray data is behind the scenes and password protected.
Gene Expression Omnibus (GEO)	http://www.ncbi.nlm.nih.gov/geo/	GEO serves as a public repository for a wide range of high-throughput experimental data.

METADATABASES

DATABASE	LINKS	DESCRIPTION
Database Overview	http://ecoliwiki.net/colipedia/index.php/Database_Overview	Information about databases.
Databases	http://ecoliwiki.net/colipedia/index.php/Databases	Information about databases.
EcoliHub	http://www.ecolihub.org/	This service allows users to quickly locate relevant information in order to make seamless bidirectional connections between E. coli resources, thereby enabling the full use of existing knowledge and supporting cutting-edge research into the molecular basis of life.
EcoliWiki	http://ecoliwiki.net/colipedia/index.php/Welcome_to_EcoliWiki	The purpose of this site is to generate community-based pages about everything related to E. coli K-12, its phages, plasmids, and mobile genetic elements.
Entrez	http://www.ncbi.nlm.nih.gov/sites/gquery	This site simultaneously search multiple life sciences databases at the National Center for Biotechnology Information (NCBI).
European Bioinformatics Institute (EBI)	http://www.ebi.ac.uk/	EBI is a portal tha gives access to the many services and research programs at the European Bioinformatics Institute.
Pathguide	http://pathguide.org/	Pathguide is a complete listing of all pathguide resources.
IECA	http://www.uni-giessen.de/ecoli/IECA/index.php	The International E. coli alliance Portal is a database that gives access to 36 databases of E. coli. It is the most recent and complete access to E.coli databases.
GenoBase (Genome Analysis Project in Japan)	http://ecoli.naist.jp/GB8/	Scope of database (GenoBase) is to understand comprehensively the living-cell system of Escherichia coli K-12 (W3110). Untill now, GenoBase is the public repository for Sequence Information, Proteome, Transcriptome, Bioinformatics, and Knowledge based on literature concerning E.coli.
CMPG (Centre of Microbial and Plant Genetics). Belgium	http://bioi.biw.kuleuven.be/bioi/software.html	Site of the data integration and network inference, toold for Motif Detection and Gene expression analysis.
Biomedical : DNA, RNA and Protein Structure Databases	http://www.science.co.il/biomedical/Structure-Databases.asp	Israel Science and Technology Homepage is the national database and directory of science and technology related sites in Israel.
2012 NAR Database	http://www.oxfordjournals.org/nar/database/c/	The NAR online Molecular Biology Database Collection, has been updated and now lists 1380 databases.

LITERATURE

DATABASE	LINKS	DESCRIPTION
Web of Science	http://apps.isiknowledge.com/WOS_GeneralSearch_input.do?highlighted_tab=WOS&product=WOS&last_prod=WOS&search_mode=GeneralSearch&SID=Y2e5IBa5M@c8B6cDO79	Explore top high-impact journals with powerful tools, such as cited reference searching and Author Finder. 256 categories thoroughly cover sciences, social sciences, arts, and humanities.
BioPathway Visualizer - Arizona BioPathway Visualizer	http://ai.arizona.edu/research/bioinformatics/previous.asp	This visualizer is a tool that allows users to navigate genetic regulatory pathway relations that are automatically extracted from biomedical literature.
EcoSal	http://www.ecosal.org/	A Web resource based on the classic ASM Press publication Escherichia coli and Salmonella: Cellular and Molecular Biology. Like its print-edition predecessors, EcoSal is a comprehensive, coherent archive of the entire corpus of knowledge on the enteric bacterial cell- but now it's continually expanded, updated, and revised. EcoSal is comprised by several hundred modules of information and interpretation with links to cognate sites containing extensive tabular and pictorial presentations, as well as to active databases of primary research information.
Faculty of 1000	http://www.f1000biology.com/browse/browse.asp?type=my&	The expert guide to the most imortant advances in biology. Select journals.
GenBank	http://www.ncbi.nlm.nih.gov/Genbank/index.html	GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.

OTHERS

DATABASE	LINKS	DESCRIPTION
A CLassification of Mobile Genetic Elements (ACLAME)	http://aclame.ulb.ac.be/	This site has a collection and classification of mobile genetic elements (phage genomes, plasmids and transposons).
BRC central	http://pathogenportal.org/portal/portal/PathPort/Home	Pathogen data repository, linking to eight Bioinformatics Resource Centers (BRCs).
CBS Genome Atlas	http://www.cbs.dtu.dk/services/GenomeAtlas/	This Atlas is a method of visualising structural features within large regions of DNA.
Essential genes in E. coli	http://www.genome.wisc.edu/resources/essential.htm	A list of genes essential for viability of E. coli.
GenoBase	http://ecoli.aist-nara.ac.jp/GB5/search.jsp	GenoBase is the public repository for Sequence Information, Proteome, Transcriptome, Bioinformatics, and Knowledge based on literature concerning E. coli.
OGeR	http://oger.tu-bs.de/	Open Genome Resource for comparative analyses of prokaryotic genomes. OGeR is an open source system for the storage, visualization and analysis of prokaryotic genome data. It provides a local or distributed data management solution for small and medium-sized sequencing projects. OGeR was developed for the comparative analysis of several related bacterial genomes. It displays homologous proteins and compares adjacent intergenic regions. Homologous regions are displayed either as a map or as multiple alignments.
microbesonline	http://www.microbesonline.org/	Publicly available suite of Web-based comparative genomic tools designed to facilitate multispecies comparison among prokaryotes.
E. coli Genome Project at the University of Wisconsin-Madison. Resources on the Internet. collections	http://www.genome.wisc.edu/resources/internet.htm#ecoli	The site provides links to research resources beyond of the E. coli Genome Project at the University of Wisconsin-Madison. The type of links are: On the campus; E. coli Related Resources (General E. coli information, and Databases and data collections); other Enterobacterial Genome Projects; and Microarray and Functional Genomics.
E. coli Genetic Resources at Yale (CGSC) The Coli Genetic Stock Center	http://cgsc.biology.yale.edu/	The CGSC Collection contains only non-pathogenic laboratory strains, primarily genetic derivatives of Escherichia coli K-12, the laboratory strain widely used in genetic and molecular studies. The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. The public version of the database includes this information and can be queried directly via this CGSC DB WebServer. For help, use the help links located above and on each query form, or contact us, as indicated below.
E. coli Statistics (CyberCell DataBase)	http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi	The CyberCell database (CCDB) is a comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli (strain K12, MG1655). The CCDB database is actually several databases, one (CCDB) contains quantitative proteomic, genomic and metabolic information about E. coli. The CC3D database contains 3D structural data for E. coli structural proteomics work, the CCRD database contains detailed information on E. coli RNA molecules while the CCMD database contains quantitative information on E. coli metabolites.
DEPPDB	http://deppdb.psn.ru/	There are some features and peculiarities of the electrostatic potential of genome DNA that correspond to its biological functions. DEPPDB and its tools provides material and facilitates analysis to study all these features and correspondences.
TBDB	http://www.tbdb.org/	The Tuberculosis Database (TBDB) is an online database providing integrated access to genome sequence, expression data and literature curation for TB.