Resources for Research and Bioinformatics
jump to organism-specific databases or general interest databases or pathogen images
Cells, Reagents, Microarrays
^topThe Biodefense & Emerging Infections Research Resources Repository provides bacterial strains, antibodies, other proteins, and DNA to registered investigators.
The American Type Culture Collection provides bacterial strains and genomic DNA for many of the sequenced strains.
The Weihenstephan Microbial Strain Collection contains many strains of food borne pathogens, specializing in Listeria and Staph among others.
The Network on Antimicrobial Resistance in Staphylococcus aureus (NARSA) provides strains exhibiting reduced susceptibility to vancomycin and other clinically important characteristics to registered investigators.
The Lancefield Streptococcus Collection contains nearly all of the strains collected by Dr. Lancefield during her career at The Rockefeller Institute. Of foremost interest are the M serotype reference strains, on which serotyping group A streptococci is based.
The BCCM/LMG public collection provides thousands of bacterial strains of medical or veterinary importance and biotechnological interest including Campylobacter, enterococci, streptococci, and Vibrionaceae.
The Pathogen Functional Genomics Resource Center, funded by NIAID, provides microarrays, protein expression clones, genotyping and bioinformatics services for both exploratory/developmental research projects and established research projects. Included among the available microarrays are Listeria monocytogenes, Staphylococcus aureus, Streptococcus pneumoniae, and Vibrio cholerae.
The Bacterial Microarray Group at St George's, University of London (BµG@S) will make available whole genome microarrays for twelve bacterial pathogens to groups around the UK and the rest of Europe. Included are Campylobacter jejuni, Listeria monocytogenes, Staphylococcus aureus, and Streptococcus pneumoniae.
Organism-specific Databases
^topCampylobacter
C. jejuni genome projects at NCBI
Comparison of multiple Campylobacter genomes at NCBI
Microarrays available in UK and Europe from BµG@S
CampyDB for comparative analysis of Campylobacter genomes
The Campylobacter Multi Locus Sequence Typing database MLSTListeria
Listeria genome projects at NCBI
Genome projects at Unité GMP, Institut Pasteur
Genome projects at the Broad Institute
Strain descriptions at the Broad Institute
Microarrays available in US from NIAID
Microarrays available in UK and Europe from BµG@S
Listilist for comparative analysis of Listeria genomes
The Listeria monocytogenes Multi Locus Sequence Typing database MLSTStaphylococcus
S. aureus genome projects at NCBI
Comparison of multiple Staphylococcus genomes at NCBI
Microarrays available in US from NIAID
Microarrays available in UK and Europe from BµG@S
The Staphylococcus aureus Multi Locus Sequence Typing database MLSTStreptococcus
S. pyogenes genome projects at NCBI
Comparison of multiple Streptococcus genomes at NCBI
The S. pyogenes Multi Locus Sequence Typing database MLST
The emm sequence database (with protocols) at the CDC Streptococcus LaboratoryS. pneumoniae genome projects at NCBI
S. pneumoniae genome projects in progress at Sanger
S. pneumoniae capsular polysaccharide (cps) loci sequences
Microarrays available in US from NIAID
Microarrays available in UK and Europe from BµG@S
The S. pneumoniae Multi Locus Sequence Typing database MLSTLaboratory of Bacterial Pathogenesis and Immunology at The Rockefeller University
S. agalactiae genome projects at NCBI
Microarrays available in US from NIAID
The S. agalactiae Multi Locus Sequence Typing database MLSTVibrio
V. cholerae genome projects at NCBI
Microarrays available in US from NIAIDV. parahaemolyticus strain RIMD2210633 genome project
V. vulnificus genome projects at NCBI
The V. vulnificus Multi Locus Sequence Typing database MLSTVibrio genome project at TIGR Microbial Sequencing Center
The Association of Vibrio Biologists and Vibrio2005
Database Resources of General Interest
Sequences and Features:
The SEED: A database of all publicly available genomes with curated subsystems as well as a host of tools that can be used to edit the functional annotations of genes or to create a subsystem that describes your work.
NCBI: National Center for Biotechnology Information, a comprehensive resource for molecular biology information, including GenBank, PubMed, Taxonomy Browser, and BLAST.
Uniprot: Universal Protein Resource, a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
Integr8: Integrated information about deciphered genomes and their corresponding proteomes.
Pathways, Reguatory Sites and Models:
Boehringer-Mannheim Wall Charts: Browse electronic versions of the Metabolic Pathways or Cellular and Molecular Processes charts at ExPASY.
The SEED: A database of all publicly available genomes with manually curated subsystems as well as a host of tools that can be used to edit the functional annotations of genes or to create a subsystem that describes your work.
KEGG: Kyoto Encyclopedia of Genes and Genomes, integrating knowledge of biological systems, genes and proteins, and chemical compounds and reactions.
EcoCyc: Literature-based curation of the genome, transcriptional regulation, transporters, and metabolic pathways of Escherichia coli K-12 MG1655.
MetaCyc: A database of nonredundant, experimentally elucidated metabolic pathways.
PUMA2: High throughput comparative and evolutionary analysis of genomes and metabolic networks with Grid computational backend
EMP: Enzymes and Metabolic Pathways database, covering all aspects of enzymology and metabolism, curated from more than15,000 publications.
RegTransBase: A manually curated database of regulatory interactions in prokaryotes, captures the knowledge in published scientific literature using a controlled vocabulary.
BioModels Database: A data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.
Enzymes, Transporters and other functions:
Brenda: Data on enzyme function extracted directly from the primary literature and maintained at the Institute of Biochemistry at the University of Cologne.
The Enzyme List: IUBMB Enzyme Nomenclature
Transport Links: Milton Saier's site classifies many if not all transport systems in a variety of species.
TransportDB: A relational database describing the predicted cytoplasmic membrane transport protein complement in completly sequenced genomes.
Immune Epitope Database and Analysis Resource: IEDB contains data related to antibody and T cell epitopes of pathogen proteins generated in humans, non-human primates, rodents, and other animal species.
^topPictures of pathogens:
PHIL, CDC: Public Health Image Library offers an organized, universal electronic gateway to CDC's pictures. Public health professionals, the media, laboratory scientists, educators, students, and the worldwide public are welcome to use this material for reference, teaching, presentation, and public health messages. The content is organized into hierarchical categories of people, places, and science, and is presented as single images, image sets, and multimedia files.
Dennis Kunkel Microscopy, Inc.: The science image library holds over 1,500 light microscopy images and electron microscopy images (colorized and black & white) taken by Dennis Kunkel Ph.D.
CELLS alive!: Film and computer-enhanced images of immune cells, bacteria, parasites, and aquatic organisms for education and medical research taken by Jim Sullivan Ph.D.
New Russell Kightley Media: Scientific Illustration & Science Animation. Copyrighted materials including still and animated images as well as interactive puzzles. Academic licenses available for people who work or study in an educational institution such as a school, college or university.