Links to important databases, tools and related projects:

Microbial Genome Sourcess

NCBI - Microbial Genomes

EBI - Genomes Pages - Bacteria

EBI - Genome Reviews

CJI - Microbial Genomics

JGI - Integrated Microbial Genomes (IMG)

JCVI - Comprehensive Microbial Ressource (CMR)

DDBJ - Genome Information Broker (GIB)

CyanoBase: Genome Database of Cyanobacteria

Sanger Institute Bacterial Genomes

GenoList genome browser

GOBASE: The Organelle Genome Database

GOLD: Genomes OnLine Database

Microbes Online

MBGD: Microbial Genome Database

PEDANT Database

Proteins and Proteomics

UniProt Database

STRING: Search Tool for the Retrieval of Interacting Genes/Proteins

PIR - Protein Information Ressource

ExPasy Proteomics Tools

Integr8 : Complete Genomes and Proteomes

NCBI Protein Database

PDB: Protein Data Bank

Gene Regulation Databases

RegTransBase

Codon Usage Database

DPInteract (Escherichia coli)

DBTBS (Bacillus subtilis)

gene-regulation.com

NDB: DNA-Binding Protein Search

PRODORIC

PromEC (E. coli promotors)

Regulon DB (Escherichia coli)

Metabolic Pathways

Boehringer Mannheim Biochemical Pathways

EcoCyc: E. coli Genes and Metabolism

KEGG: Kyoto Encyclopedia of Genes and Genomes

MetaCyc: Encyclopedia of Metabolic Pathways

UM-BDD - Microbial Biocatalytic Reactions and Biodegradation Pathways

BRENDA: The Comprehensive Enzyme Information System

DNA Pattern Search

AlignACE: Motif finding algorithm

Virtual Footprint

NNPP: Neural Network Promoter Prediction

RSA-Tools: Regulatory Sequence Analysis

Improbizer: Search for motifs with improbable frequency

Signal Scan: Matrix Search Tool

TESS: Transcription Element Search

Protein Domain, Motif and Signature Search

Blocks Server

MAST: Motif Alignment and Search Tool

MEME: Multiple EM for Motif Elicitation

MOTIF: Sequence Motif Search

PatScan: Pattern Scan

Pfam: Protein Families

PRINTS: Protein Fingerprint Database

ProDom: Protein Domain Database

PROSITE: Database of protein families and domains

Smart: Simple Modular Architecture Research Tool

Sequence Analysis (DNA & Proteins)

ExPasy Proteomics Tools

FramePlot: Frame Analysis

ORF Finder (NCBI): Gene Prediction

Repeat Masker: Search for Repetitive Elements

Reverse Complement

Sequence Format Conversion

SignalP: Signal Peptide Cleavage Sites

TMHMM: Prediction of Transmembrane Helices

TMpred: Prediction of Transmembrane Regions

Alignment and Phylogenetic analysis

BLAST: Basic Local Alignment Search Tool

BOXSHADE: Pretty Printing of Alignments

CLUSTALW: Multiple Alignment

PHYLIP: Free Package of Phylogeny Programs

MUSCLE: Protein Multiple Sequence Alignment Software

SIM: Pairwise Alignment

T-COFFEE: Multiple Alignment