Resources for Research and Bioinformatics

Cells, Reagents, Microarrays

Biodefense & Emerging Infections Research Resources Repository provides bacterial strains, antibodies, other proteins, and DNA to registered investigators.

American Type Culture Collection supplies bacterial strains and genomic DNA for many of the sequenced strains.

Weihenstephan Microbial Strain Collection contains many strains of food borne pathogens, specializing in Listeria and Staph among others.

Network on Antimicrobial Resistance in Staphylococcus aureus (NARSA) provides strains exhibiting reduced susceptibility to vancomycin and other clinically important characteristics to registered investigators.

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.

BCCM/LMG public collection supplies thousands of bacterial strains of medical or veterinary importance and biotechnological interest including Campylobacter, enterococci, streptococci, and Vibrionaceae.

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. The available microarrays include all NMPDR core organisms: Campylobacter jejuni, Listeria monocytogenes, Staphylococcus aureus, Streptococcus pneumoniae, S. pyogenes, and pathogenic Vibrios.

The Bacterial Microarray Group at St George's, University of London (BG@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.

^top

Organism-specific Databases

Campylobacter

C. jejuni genome projects at NCBI
Comparison of multiple Campylobacter genomes at NCBI

Microarrays available in UK and Europe from BG@S
CampyDB for comparative analysis of Campylobacter genomes
The Campylobacter Multi Locus Sequence Typing database MLST

Listeria

Listeria genome projects at NCBI
Genome projects at Unit 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 BG@S
Listilist for comparative analysis of Listeria genomes
The Listeria monocytogenes Multi Locus Sequence Typing database MLST

Staphylococcus

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 BG@S
The Staphylococcus aureus Multi Locus Sequence Typing database MLST

Streptococcus

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 Laboratory

S. 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 BG@S

The S. pneumoniae Multi Locus Sequence Typing database MLST

Laboratory 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 MLST

Vibrio

V. cholerae genome projects at NCBI
Microarrays available in US from NIAID

V. parahaemolyticus strain RIMD2210633 genome project

V. vulnificus genome projects at NCBI
The V. vulnificus Multi Locus Sequence Typing database MLST

Vibrio genome project at JCVI Microbial Sequencing Center

The Association of Vibrio Biologists

^top

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, Tr EMBL? , 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

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.

Pictures 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.

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.

Visuals Unlimited: Images "from photomicrographs to world biomes." A collection of copyrighted works of hundreds of talented professional, scientific, medical, and natural history photographers worldwide.

Topic revision: r5 - 15 Feb 2009 - 17:50:15 - TWiki Guest
 
Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.