The Hancock Lab List of Links

From the R.E.W. Hancock Laboratory. Also check out our list of "Cool Microbiology Web Sites".

• DNA and protein sequence databases, analysis and reference
• Genome Centres
• Bioinformatics and Informatics
• Centers and sites dealing with microbiological disease and general microbiology issues
• Profile: Antibiotic resistance
• Journals, Other Publications, Patent Search, and Newsgroups
• Local
• Other colleges and universities
• Web search and other reference
• Links to a few pages having a more comprehensive list of relevant web sites

DNA and protein sequence databases, analysis and reference
- BCM (Baylor College of Medicine) Search Launcher
- BCM ClustalW sequence alignment
- BLOCKS - compare against a database of sequence blocks
- ChemFinder
- CN3D and VAST - structure viewer and search for 3D structure similarity
- Codon Usage Database
- E. coli Genome Center (U. Wisconsin)
- E.coli index
- EBI - European Bioinformatics Institute (ClustalW, Fasta and much more...)
- EcoCyc and MetaCyc: pathways/genes databases (free registration)
- EMBL
- EMBL ClustalW sequence alignment
- EMBL sequence analysis programs, including transmembrane prediction
- Enterix (and Menterix and Maj)
- ENZYME: ExPASy's enzyme nomenclature database (contains pathways too)
- ExPASy - Canada Mirror Site
- ExPASy Proteomics Tools (and more!)
- FPAT - search protein databases for patterns
- GeneCards: human genes, proteins and diseases
- Genedoc
- GeneMark.HMM gene prediction
- Glimmer gene prediction
- k2d (protein secondary structure prediction from CD spectra)
- KEGG - Kyoto Encyclopedia of Genes and Genomes
- Klotho: Biochemical Compounds Declarative Database
- Macromolecular Museum
- MIPS - PEDANT, MITOP, Orpheus
- NCBI - Compare against COGs database (see above for other NCBI sites)
- NCBI-BLAST (Includes human PSI, PHI, "compare 2 sequences", and special database searches)
- NCBI-Entrez
- NCBI-old advanced BLAST page
- NCBI-Taxonomy Browser
- NCBI-Unfinished Microbial Genomes BLAST
- OMIM - Cystic Fibrosis entry
- Orpheus (under MIPS)
- OWL - strictly non-redundant composite of selected protein databases
- Pathogenomics Project
- PDB (Protein Data Bank)
- PEDANT (under MIPS)
- PFAM
- PHYLIP
- PhyloBLAST
- Polysaccharide Genes Database
- PRINTS
- ProFound
- PROPSEARCH (search proteins by amino acid composition)
- PROSITE scan
- Protein Molecular Weight and pI determination
- PseudoCAP Sequence Analysis Tools
- Pseudomonas Genome Database at the University of Queensland
- Pseudomonas Genome Project Genome Database
- PSORT - Predicts protein localization within cells
- PubCrawler - "It goes to the library. You go to the pub."(tm)
- RasMol (more recent version)
- RasMol and Chime - Molecular Visualization Freeware
- Ribosomal Database Project
- Russian Server for Sequence Analysis Programs
- Sequence alerting (be notified when a new sequence comes out that has similarity to your sequence of interest)
- SignalP: signal sequence prediction and cleavage
- SRS - Sequence Retrieval System - EBI site
- SwissModel
- Taxonomy Browser (NCBI)
- The Bacterial "Code" (NCBI's translation table 11 and notes)
- TIGR's Microbial Genome Projects List
- Transporters in Prokaryotes: Genomic Analysis
- VectorDB
- Webcutter (for restriction enzyme analysis)
- WIT (a metabolic pathways reference page - free registration)
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Genome Centres
- Baylor College of Medicine
- CBC - U Minnesota
- DOE Joint Genome Institute (JGI)
- Genome Sequence Center, Washington University
- Genome Sequence Centre, BC Cancer Agency
- Heidelberg
- Jackson Labs
- More Genome Centres...
- NITE
- Oklahoma U - ACGT
- Sanger Centre
- Stanford
- TIGR
- U Washington Genome Center, Seattle
- U Wisconsin
- Whitehead Institute for Biomedical Research/MIT Center for Genome Research
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Bioinformatics and Informatics
- Biocatalog - EBI Mol. Bio. Software
- Bioinform - "The Global Bioinformatics News Service"
- Bioinformatics (journal)
- Bioperl Project
- Canadian Bioinformatics Resource
- Canadian Bioinformatics Workshop
- CCP11's Bioinformatics Resource
- HGMP list of bioinformatics programs
- HTML - The Basics
- International Society for Computational Biology
- Jong Park's Perl Subroutine Library - Bio.pl
- Journal of Computational Biology
- Journals: List of Journals Relevant to Bioinformatics
- Molecular Linux
- PERL reference
- Phylip documentation
- SAL - Scientific Applications on Linux
- Unix - More Basics from the UW Genome Sequence Centre
- Unix - The Basics
- Unix Guru Universe
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Centers and sites dealing with microbiological disease and general microbiology issues
- A Complete OnLine Microbiology Textbook
- American Society for Microbiology
- American Type Culture Collection Homepage
- Another Microbiology Textbook - From Washington State
- Antimicrobial Peptide Website
- Antimicrobial peptides - literature references
- Antimicrobial Sequences Database
- Bad Bug Book
- BC biotechnology alliance
- BioMedNet (free registration)
- Biospace.com
- Bugs in the News
- Canadian Bacterial Diseases Network
- Canadian Biotechnology Strategy
- Canadian Cystic Fibrosis Foundation
- Canadian Institutes of Health Research
- Canadian Society of Microbiologists
- CellsAlive!
- Centers for Disease Control and Prevention
- Centre for Microbial Diseases and Host Defense Research (CMDR)
- CF-WEB
- CommonCold.org
- Cystic Fibrosis Foundation
- E. coli genetic stock center
- E.coli index
- EcoCyc: E. coli genes, metabolism/pathways reference
- Health Canada
- ID Links: Communication Center for Infectious Disease and Outpatient Care
- Laboratory Centre for Disease Control (includes feature to make charts of data on reportable diseases)
- Microbial Genomes Mailing List
- Microbial underground
- Microbiology Courses on the Web
- NIH
- NSERC
- Pan American Health Organization
- Transporters in Prokaryotes: Genomic Analysis
- Tree of life home page
- United Nations
- World Health Organization
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Profile: Antibiotic resistance
- "The Challenge of Antibiotic Resistance" (in SCIAM) By Stewart Levy
- Alliance for the Prudent Use of Antibiotics
- Animicrobial Peptide Website
- Resistance Web
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Journals, Other Publications, Patent Search, and Newsgroups
- Academic Press Journals
- AIP/APS Virtual Journal of Biological Physics Research
- Annual Review of Microbiology
- Antimicrobial Agents and Chemotherapy
- ASM journals
- Biochemistry
- Biochimica et Biophysica Acta (BBA)-General Subjects
- BioEssays
- Bioinformatics
- BioMedNet
- BIOSCI/bionet
- BioTechniques
- Canadian Journal of Microbiology and other NRC journals
- Canadian Patent Index
- Cell
- Current Opinion in Immunology
- Current Opinion in Microbiology
- EMBO
- Emerging Infectious Diseases
- Evolution
- FEBS Letters
- FEMS Microbiology Letters
- FEMS Microbiology Reviews
- Gene
- Genome Research
- Genomics
- Immunity
- Infection and Immunity
- Journal of Bacteriology
- Journal of Biological Chemistry
- Journal of Clinical Microbiology
- Journal of Computational Biology
- Journal of Immunology
- Journal of Molecular Biology
- Journal of Molecular Evolution
- Microbial Genomes Mailing List
- Microbiology and Molecular Biology Reviews
- Molecular and Cellular Biology
- Molecular and General Genetics
- Molecular Biology and Evolution
- Molecular Microbiology
- Nature
- Nature Biotechnology
- Nature Structural Biology
- Nucleic Acids Research
- PNAS
- Science
- Scientific American
- Trends in Biochemical Sciences
- Trends in Biotechnology
- Trends in Immunology
- Trends in Microbiology
- UBC library - Elsevier Science Collection of Online Journals (for UBC only)
- UBC library - Full Text of Selected Journals Online (for UBC only)
- UBC library - OVID Medline and Current Contents Searches (for UBC only)
- US patent search (from IBM)
- US patent search (from qpat)
- Virtual Library - includes other journals...
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Local
- BC biotechnology alliance
- BC Centre for Disease Control
- BC Centre for Integrated Genomics
- BC Ferries Info and Schedules
- BC Transit - Bus, Skytrain etc... info
- Centre for Microbial Diseases and Host Defense Research (CMDR)
- Centre for Molecular Medicine and Therapeutics (CMMT)
- Discover Vancouver
- Environment Canada Weather Forecast for Vancouver
- Genome Sequence Centre, BC Cancer Agency
- ISI's Web of Science Citation Databases (UBC has an account)
- Linux in BC
- Microbiology and Immunology Dept. homepage
- MyBC (Includes interactive local maps, BC Yellowpages and whitepages/PeopleFinder)
- Pathogenomics Project
- Peter Wall Institute For Advanced Studies
- PhyloBLAST - new tool!
- Simon Fraser University
- UBC campus maps
- UBC homepage
- UBC library
- UBC library - Elsevier Science Collection of Online Journals (for UBC only)
- UBC library - Full Text of Selected Journals Online (for UBC only)
- UBC library - OVID Medline and Current Contents Searches (for UBC only)
- UBC Research Services
- UBC Travel Program
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Other colleges and universities
- Listing of all College and University Homepages
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Web search and other reference
- A Web of On-Line Dictionaries (links to Dictionaries for many different languages)
- Altavista
- Altavista's Web Page Translation
- Homefair.com (stats on cities etc...)
- ISI's Web of Science Citation Databases (UBC has an account)
- On-Line Medical Dictionary
- Periodic Table
- Travlang's Languages for Travellers (hear how to say phrases in different languages)
- UK detailed maps and hotel guide
- Units Conversion
- USA Hotel Guide
- World Atlas Online
- Yahoo
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Links to a few pages having a more comprehensive list of relevant web sites
- Andy Kropinski's Online Analysis Tools (excellent resource for those new to sequence analysis)
- BCM's list of links
- Biology Links: Evolution
- Bioplanets Links
- Bork Group's Hotlist (they check for dead links every day)
- GenomeWeb
- HGMP list of bioinformatics programs
- Microbiology Courses on the Web
- Molecular Biology Jump Station
- RNA links
- Shaun Black's page
- Virtual Library - includes other journals...
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