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See also
Science Magazine - Special Online Collection: The SARS Epidemic
"The molecular biology of the coronavirus that causes severe acute respiratory syndrome (SARS) comes into clearer focus this week, with the online publication, on Science Express, of two papers that provide initial analysis and characterization of the SARS virus genome. Science is making these important papers, along with an accompanying editorial, free to all visitors."[All additional SARS resources available on a "pay-per-article" basis.]
Genome Gateway
"...a comprehensive web resource devoted to genomics. Access is free and the Gateway will provide: A library of original research papers, including all genome-related papers from Nature and Nature Genetics plus links to other major publications. Relevant News and Views articles are also provided. A news service from Nature and Nature Genetics, providing up-to-the-minute coverage of research progress, policy issues, funding and ethical implications of genome sequencing. A post-genomics section, covering the myriad applications of sequencing research and the technologies. A set of links to the most useful and informative genomics sites on the web."
Nature Genome Information Centre
123 Genomics
Genomics and Bioinformatics Resources
Sections include: Learning ; Databases ; Analysis ; Diseases & Disorders ; Genes & Proteins ; Population Genetics ; Molecular Pathways ; Methods & Protocols ; News ; Publications ; Courses ; Organizations ; Conferences ; Jobs ; Computer Resources ; Companies.
BioCyc Knowledge Library
"...is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism, with the exception of the MetaCyc database, which is a reference source on metabolic pathways from many organisms...The BioCyc databases are electronic reference sources for biologists who work with various microorganisms. Currently, detailed organism-specific information is available for 13 species. In addition, the MetaCyc metabolic pathway database contains data from 150 species."
Centers for Disease Control and Prevention (CDC)
Clemson University - Genomics Institute
The Comprehensive Microbial Resource Home Page
"These pages have been designed to allow the user to access data from all of the genome sequences completed to date. Accessible here is the Omniome database which contains the sequence and annotation of each of the completed genomes as well as associated information about the organisms (such as taxon and gram stain pattern), the structure and composition of their DNA molecules (such as plasmid vs. chromosome and GC content), and many attributes of the protein sequences predicted from the DNA sequence (such as pI and molecular weight)."
The Institute for Genomic Research
DOE Joint Genome Institute (JGI)
Operated by The University of California for The US Department of Energy
Dolan DNA Learning Center - Genes in Education
"The mission of the Dolan DNA Learning Center is to prepare students and families to thrive in the gene age. We envision a day when all elementary students are exposed to principles of genetics and disease risk; when all high school students have the opportunity to do hands-on experiments with DNA; and when all families have access to genetic information they need to make informed health care choices."
- Cold Spring Harbor Laboratory
European Bioinformatics Institute (EBI)
- CluSTr
"...(Clusters of SWISS-PROT+TrEMBL proteins) database offers an automatic classification of SWISS-PROT + TrEMBL proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. The database provides links to InterPro, which integrates information on protein families, domains and functional sites from PROSITE, PRINTS, Pfam, ProDom, SMART and TIGRFAMs. CluSTr also has cross-references to HSSP and PDB...is a useful resource for whole genome analysis and has already been used for the proteome analysis of a number of completely sequenced genomes. A preliminary proteome analysis was also produced for the human genome."
- Parasite Genome Internet Resources
"This page links to www sites, ftp and gopher sites, email networks and genome project secretaries or other contacts for all the WHO and other parasite genome projects."
Genome Biology
"Genome Biology publishes commentaries, reviews, and original research. The original research articles are provided below free of charge. The full contents of Genome Biology are available on a subscription basis..."
The Genome Channel
Includes data, tables, and summaries
Computational Biosciences Section - (dead link), Oak Ridge National Laboratory
Genome Research
"The journal focuses on genome studies in all species, and presents research that provides or aids in genome-based analyses of biological processes. The journal represents a nexus point where genomic information, applications, and technology come together with biological information to create a more global understanding of all biological systems. "
Occasionally special issues are available with free online content.
Genomes & Machines
"In this page you will find links to the most representative genomic databases and tools, tutorials, data and software providers, public and private research centres, relevant paper references, reviews on articles and products, etc."
By Francisco Azuaje, Dept. of Computer Science, The University of Dublin, Trinity College
Genomics and Its Impact on Medicine and Society: A 2001 Primer
Human Genome Program, U.S. Dept. of Energy
Genomics Glossary
By Mary Chitty, Library Director, Cambridge Healthtech Institute
GOBASE - The Organelle Genome Database
"GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to organelles. The new version focuses on the mitochondrial and chloroplast subset of data. In its next phase, GOBASE will also include information on representative bacteria that are thought to be specifically related to the bacterial ancestors of mitochondria and chloroplasts."
- Departement de Biochimie, UniversitÈ de MontrÈal.
ImMunoGeneTics (IMGT) Database - (dead link)
"...is a high-quality integrated information system specialising in Immunoglobulins (IG), T cell receptors (TR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species...consists of sequence databases (IMGT/LIGM-DB, a comprehensive database of IG and TR from human and other vertebrates, with translation for fully annotated sequences, and IMGT/HLA-DB, a database of the human MHC), genome and structure databases (IMGT/3Dstructure-DB), Web resources (IMGT Marie-Paule page) and interactive tools. The IMGT server provides a common access to all Immunogenetics data."
The Institute for Genomic Research (TIGR)
[12th] International Genome Sequencing and Analysis Conference
The Institute for Gnomic Research (TIGR)
September 12-15, 2000; Miami Beach, Florida, USA.
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."
Bioinformatics Center, Institute for Chemical Research, Kyoto University
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Mitochondria Project (MITOP)
Database for mitochondria-related genes, proteins and diseases.
MITOP offers specific search facilities subdivided into functional category classification, protein classes and complexes, subcellular localizations, EC numbers, molecular weight and isoelectric points, Prosite motifs and non-protein entries. It includes a homology search for each protein using a precomputed FASTA."
Search: Human ; Mouse ; Yeast ; C. elegans ; N. crassa
- Munich Information Center for Protein Sequences (MIPS)
National Academy Press (free downloads)
National Center for Biotechnology Information (NCBI)
- National Institutes of Health
- Entrez Popset
"A PopSet is a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The population could originate from different members of the same species, or from organisms from different species."
- Gene Expression Omnibus(GEO)
"GEO is our effort to build a gene expression data repository and online resource for the retrieval of gene expression data from any organism or artificial source."
- Reference Sequence (RefSeq)
"The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms...RefSeq standards serve as the basis for medical, functional, and diversity studies; they provide a stable reference for gene identification and characterization, mutation analysis, expression studies, polymorphism discovery, and comparative analyses. RefSeqs are used as a reagent for the functional annotation of some genome sequencing projects, including those of human and mouse."
- Viral Reference Genomes - (dead link)
"This collection of virus genomic sequences is a part of the Entrez Genomes that provides curated sequence data and related information for the community."
Nature [Magazine] Genome Gateway
"...special section of the Genome Gateway to mark the publication of the initial sequencing and analysis of the human genome. We are delighted to uphold the principle at the heart of the Human Genome Project: free and unrestricted access to all our genome related material through these web pages."
- Papers
- Ocean Genomics
"With the sequencing of microbial genomes now almost routine in some circles, one could be forgiven for feeling a little jaded. However, reports in this week's Nature powerfully demonstrate how genomics can lead to a new understanding of biodiversity, ecology and biogeochemistry. This collection, along with other analysis of key components of the ocean's food web, highlights the significance of genome sequences from the sea..."
Sanger Institute
- Sequencing Projects
Projects include: Human Genome ; Non-Human Vertebrates ; Worm ; Fungi ; Microbial Genomes ; Protozoa ; Others.
Science Functional Genomics
"...is designed to serve as a convenient entry point to the rich world of genomics and, especially, post-genomics. It includes current news, a news archive, drawn mainly from Science and ScienceNOW, a collection of research papers and news broken into various categories of interest in the post-genomic world, a page gathering together Science's genome special issues, pointers to a wide variety of Web resources in genomics and post-genomics, and a special node of news and information on the biotechnology business."
- From Science magazine
Science Magazine - Special Online Collection: The SARS Epidemic
"The molecular biology of the coronavirus that causes severe acute respiratory syndrome (SARS) comes into clearer focus this week, with the online publication, on Science Express, of two papers that provide initial analysis and characterization of the SARS virus genome. Science is making these important papers, along with an accompanying editorial, free to all visitors."[All additional SARS resources available on a "pay-per-article" basis.]
TIGR - The Institute for Genomic Research
UCSC Genome Bioinformatics
"This site contains working drafts for the human, mouse, and rat genomes...The Genome Browser and the data it displays are freely available for academic, nonprofit, and personal use with a few exceptions."
- University of California, Santa Cruz
Using Genomic Databases - (dead link)
From Current Topics in Health Sciences Librarianship.
Welch Medical Library, Johns Hopkins Medical Institutions
Xylella fastidiosa Genome Project
"...is a fastidious, xylem-limited bacterium, which causes a range of economically important plant diseases. This website contains information about the complete genome sequence of X. fastidiosa clone 9a5c, shown to cause citrus variegated chlorosis, a serious disease of orange trees. Citrus Variegated Chlorosis (CVC), which was first recorded in Brazil in 1987, affects all commercial sweet orange varieties."
See also
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