CMR Related Links

JCVI Links

CAMERA: CAMERA is a web resource for metagenomic research. CAMERA's debut coincides with the publication of the Global Ocean Sampling expedition's extensive dataset cataloging over 6 million new genes from uncultured marine microbes. Come visit CAMERA, and see our growing collection of metagenomics datasets and tools.

TIGRFAMs Home Page: TIGRFAMs are protein families based on Hidden Markov Models or HMMs. Use this page to see the curated seed alignmet for each TIGRFAM, the full alignment of all family members and the cutoff scores for inclusion in each of the TIGRFAMs. Also use this page to search through the TIGRFAMs and HMMs for text in the TIGRFAMs Text Search or search for specific sequences in the TIGRFAMs Sequence Search.

TIGR Databases: The TIGR Databases are a collection of curated databases containing DNA and protein sequence, gene expression, cellular role, protein family, and taxonomic data for microbes, plants and humans.

JCVI Software Tools: JCVI is making a number of software tools freely available to the scientific community.

Publication Links

PubMed: PubMed is the National Libarary of Medicine's search service that provides access to over 11 million citations in MEDLINE, PreMEDLINE and other related databases, with links to participating online journals.

The Nature Genome Gateway: Links to all of the genome papers published in the journal Nature.

Science Functional Genomics: Science Functional Genomics is designed to serve as a convenient entry point to the rich world of genomics and, especially, post-genomics. It includes news, a collection of research papers, a page gathering together Science's genome special issues, pointers to a wide variety of scientific and educational Web resources, and a special node of news and information on the biotechnology business.

Sequence & Organism Acquisition

TIGR FTP: Download all TIGR genomes using ftp.

Genbank FTP: Download all published bacterial genomes from Genbank using ftp.

ATCC: American Type Culture Collection (ATCC) is a global nonprofit bioresource center that provides biological products, technical services, and educational programs to private industry, government, and academic organizations around the world.

Genome Databases and Analysis Sites

NCBI Home Page: The National Center for Biotechnology Information serves as a national resource for molecular biology information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information.

NCBI's COG Home Page: COGs or Clusters of Orthologous Proteins are phylogenetic classifications of proteins encoded in complete genomes. COGs were delineated by comparing protein sequences encoded in 21 complete genomes, representing 17 major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.

ISfinder: ISfinder is a dedicated database for bacterial insertion sequences. It has taken over the role of the Stanford reference center. One of its functions is to assign IS names and to provide a focal point for a coherent nomenclature. It is also the repository for IS sequences.

DNA Structural Analysis of Complete Genomes and Chromosomes: The DNA Structural Atlas is a method of visualising structural features within large regions of DNA. The idea is to plot the values for six different mechanical-structural properties of the DNA helix in a circle (or arc) representing the complete genome (or chromosome). This link takes you to the top page for the Genome Atlas where all of the organisms are listed. The next link takes you to this genome's individual genome atlas.

The Genome Channel: Shows genome information on completed genomes.

Enzyme Nomenclature Page: Enzyme Commission Numbers or EC#s are numbers assigned to enzymes that reflect their function. For more information and a complete list of all EC#s, visit the Enzyme Nomenclature Page.

Pfam Home Page: Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.

PROSITE Home Page: PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs.

European Bioinformatics Institute: European Bioinformatics Institute (EBI) is a center for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.

Swiss-Prot & TrEMBL: SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. TrEMBL is a computer-annotated supplement of SWISS-PROT that contains all the translations of EMBL nucleotide sequence entries not yet integrated in SWISS-PROT.

PEDANT: Protein Extraction, Description and ANalysis Tool or PEDANT provides genome analysis and annotation for all the genomes that have been sequenced.

KEGG: Kyoto Encyclopedia of Genes and Genomes: Kyoto Encyclopedia of Genes and Genomes (KEGG) is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene catalogs produced by genome sequencing projects.

Paulsen Transporter Page: A site that provides the genomic comparison of membrane transport systems.

WIT: What Is There?: WIT is a www-based system to support the curation of function assignments made to genes and the development of metabolic models.

Genome Information Broker (GBI) for Microbial Genomes: GIB compiled the International Nucelotide Sequence Database (DDBJ/EMBL/GenBank) entries that had been submitted by microbial genome project teams worldwide into databases specific to the species. Users are able to use the numbers and names of clones, ORFs and genes, and sequences to retrieve the data in the database. Results are represented in interactive graphics and tables.

Indigo: A comprehesive site that displays detailed analyses and information on both the E.coli and B.subtilis genomes.

MBGD: Microbial Genome Database (MBGD) is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly. The aim of MBGD is to facilitate comparative genomics from various points of view such as orthologue identification, paralogue clustering, motif analysis and gene order comparison.

High quality Automated Microbial Annotation of Proteomes (HAMAP): The ExPASy HAMAP project aims to automatically annotate a significant percentage of proteins originating from microbial genome sequencing projects. In order to maintain a high level quality of annotation, tools that are being developed specifically deal with two completely separate subsets of bacterial and archaea proteins: (1) Proteins that have no recognizable similarity to any other microbial or non-microbial proteins. (2) Proteins that are part of well-defined families or subfamilies.

ARCHAebacterial Information Collection (ARCHAIC): The aim of ARCHAIC is to analyze archaebacterial genomic DNA sequences in order to understand the overall organization of these genomes and in order to permit comparison of different species on the basis of their genomic DNA sequences.

Los Alamos National Lab: The LANL specialized databases includes molecular information pertaining to sexually transmitted bacteria and viruses -- especially, though not limited to, molecular sequence data.

General Links

The DEAMBULUM: Provides many helpful links for each sequenced genome.

Medical Microbology: A comprehensive on-line textbook of microbiology.

The Bad Bug Book: The U.S. Food and Drug Administration Center for Food Safety & Applied Nutrition Foodborne Pathogenic Microorganisms and Natural Toxins Handbook. This handbook provides basic facts regarding foodborne pathogenic microorganisms and natural toxins. It brings together in one place information from the Food & Drug Administration, the Centers for Disease Control & Prevention, the USDA Food Safety Inspection Service, and the National Institutes of Health.

ScienceNet: The ScienceNet profiles section contains a series of profiles in which each organism's particular features are presented as short paragraphs listing their characteristics. The same set of headings are used for all organisms, so that rapid comparisons can be acheived.