Goldman Group Links

Initial Guess

• EBI
• Sanger Centre
• NCBI (Entrez, BLAST, GenBank,...)
• Bio-software Archive
• ABim
• Robison
• WWW-VL
• Human Genome
• Expasy

On-line Analysis Servers

• BLOCKS
• MFOLD

DNA Data

• GenBank Database
• GenBank Latest Release Information
• BankIt - Information on submitting sequences to GenBank
• DDBJ - DNA Data Bank of Japan

Protein Data

• The OWL Database - Non-redundant protein database
• PIR Databases - Protein Indentification Resource
  
• PDB - Protein Data Bank (at Brookhaven National Laboratory)

Protein Structure Prediction

• Cambridge Crystallographic Data Centre

Protein Structure Data

• MODELLER : homology modelling program by satisfaction of spatial restraints
• SWISS-MODEL (part of ExPasy server)
• H3P2 : Rice threading approach
• topITS
• THREADER
• DPM (Double Prediction Method)
• DSC : secondary structure prediction
• GOR (Soton)
• MultPredict (also known as ZPRED)
• NNPREDICT
• PREDATOR
• PSA : probabilistic folding class, secondary and supersecondary structure prediction
• SSCP
• TMAP

Other Databases

• PFAM (Cambridge)
• YPD (Yeast Protein Database)
• Small RNA database at Baylor
• de Wachter rRNA database
• RNA World
• The Tree of Life phylogeny page.
• FASTA searches
• LPFC protein family cores (Mark Gerstein)
• Yeast Gene Duplications (Wolfe and Shields)
• RepeatMasker (Arian Smit)
• Protein Kinase Resource (Hanks, UCSD)
• The Genome Database - Supporting the Human Genome Project
• Medline Query Form - Medline is an excellent bibliographic database
• Jacobson' archive at J.Hopkins University
• GENATLAS The GENATLAS database
• Homology Data Home page of Professor John Edwards
• Weizmann Institute Chromosome 17 database/integrated map
• Whitehead Institute Includes the YAC-STS mapping project
• Genetic analysis web serverGenome mapping software resources
• Cooperative Human Linkage Centre Linkage maps of the human genome
• UK MRC HGMP Resource Centre Centre for the UK Human Genome Program
• Genethon The French sequencing initiative

Genome Project Information

• Status of Genome Sequencing Projects
• Complete genomes (sequence access)
  • Mycoplasma genitalium (TIGR)
  • Haemophilus influenzae (TIGR)
  • Methanococcus jannaschii (TIGR)
  • Synechocystis PCC6803 (Kazusa, Japan)
  • Escherichia coli (Wisconsin)
  • Saccharomyces cerevisiae (consortium)
• Genome centers
  • Sanger Centre
  • Stanford
  • TIGR
  • EBI
  • NCBI

HIV - Human Immunodeficiency Virus

• HIV sequence database - At Los Alamos
• National Agency of Research on AIDS - ANRS, based in Marseilles

Codon Usage

• Information on codon usage
• CUTG - Codon Usage Tabulated from GenBank
• Correspondence Analysis of Codon Usage

Biomathematics

• The Aberystwyth quantitative biology and analytical biotechnology group
• Biolinks
• Boston University - Department of Biophysics
• Boletín Latinoamericano de Biomatemática
• The Centre for Nonlinear Dynamics in Physiology and Medicine, McGill University
• Centre for Mathematical Biology, Oxford
• CSU Bioweb
• The IMA Forum for Mathematics in Medicine and Biology (UK)
• The Institute for Mathematics and its Applications at the University of Minnesota
• The Israeli Society for Theoretical and Mathematical Biology (ISTMB)
• Mathematical Biology at Brandeis
• Mathematical Biology at the Univeristy of British Columbia
• National Institutes of Health
• The NCI Laboratory of Mathematical Biology
• Nonlinear Dynamics in Biology at UC Davis
• North Carolina State University Biomath Program
• The Sewall Wright Institute of Quantitative Biology
• The Strome Lab at Indiana University
• UTK Mathematical Life Sciences Archives

Genome Analysis/Genomic Comparisons

• PEDANT - Protein Extraction, Description, and ANalysis Tool: Lots of information on sequenced genomes
• Magpie - Containing comprehensive review of various genome sequencing projects
• TIGR - The Institute for Genomic Research
• Genomes Organism Representation - Find out about the genome of the organism of y our choice, uses Entrez
• National Center for Genome Resources

Phylogeny

• Phylip
• The Tree of Life Home Page
• NCBI Taxonomy homepage
• Phylogenetic Programs (Arizona)
• TreeView
  
  
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On-line journals, publishers and paper databases

• Bioinformatics
• In Silico Biology
• Cambridge University Press
• Current Opinion in Structural Biology
• Nature
• Proteins
• Trends in Biochemical Sciences
• Science
• Nucleic Acids Research
• The Journal of Molecular Biology
• New Scientist
• XXX at Los Alamos
• XXX at Southampton
• Correlation Analysis in DNA sequences

Bioinformatics and biotech companies

• Glaxo-Wellcome
• AstraZeneca
• Pfizer
• Eli Lilly
• NeXstar
• Time Logic
• Compugen
• Pangea
  
  
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Links to Colleagues

• David Jones
• Geoff Barton.
• Joe Felsenstein
• Andrey Rzhestky
• Michael Gribskov

Software, Web, documentation development

• comp.lang.c FAQs
• HTML
  • HTML primer
  • Advanced HTML
  • Netscape Frames tutorial
  • NCSA HTTPD
• Java
  • Java Tutorial
• LaTeX
• GNU
• Tcl
• Netlib
  
  
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Maths

• American mathematical Society
• mathematical software (1)
• mathematical software (2)
• Bayesians Worldwide
• International Society for Bayesian Analysis (ISBA)
• The Bayesian Analysis E-Print Archive
• Non-subjective Bayesian Statistical Methodology
• StatLib, Carnegie Mellon
• University of Wales Swansea, Statistics and Actuarial Studies
• UK Academic Sites
• CTI, Statistics on Web
• Mailbase
• American Statistical Association
• Institute of Mathematical Statistics

HMM, Neural Networks, Wavelets etc

• HMM
• the Mathsoft page, a collection of papers
• Wavelet Digest, a monthly newsletter
• Rice DSP group, Publications

Positions open, Funds, Fellowships, Visitors

• BBSRC Biotechnology and Biological Sciences Research Council

Utility

• London Street map, UK placenames, UK postcodes
• Dictionaries
• Cambridge area information
• Trains Timetable