CRP-DNA Complex
PRODORIC logo Release 8.9

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