Web template
updated by
Christopher Spry
2 May 2014

Molecular Biology resources

These links were derived initially in 1995 from a list in HUGO's 'Genome Digest' 2, (4) Oct 1995 pp 10-12. It is not comprehensive. Please emailChristopher Spry with URLs of other sites that you would like included. There is now (1 February 1998) a comprehensive 'links' site at Hinxton Hall, called 'The GenomeWeb'. It is far more comprehensive and up-to-date than my little effort :)

Resources listed by country: Click on one of the countries below, or use 'Edit', 'Find...'  to look for specific links:

  • Belgium
  • Canada
  • Denmark
  • Finland
  • France
  • Germany
  • Holland
  • Israel
  • Japan
  • Norway
  • Sweden
  • Switzerland
  • UK
  • USA
  • Other resources

  • Belgium

  • Brussels: Instituut voor Moleculaire Biologie en Biotechnologie
  • University of Namur,The Match-Box multiple sequence alignment method circumvents the gap penalty requirement. In the Match-Box method the gaps are the result of the alignment and not a governing parameter of the matching procedure. The method produces reliable results, as assessed by the tests performed on protein families of known structures and of low sequence similarity. A reliability score is computed in relation with a threshold of similarity progressively raised to extend the aligned regions to their maximal length. The score obtained at each position of the final alignment is printed below the sequences and allows a discriminant reading of each aligned region. Several additional outputs present pairwise similarity analyses in order to allow delineation of relevant subsets of related sequences and to avoid alignment of unrelated sequences.
  • Canada

  •  
  • Montreal
  • gopher to the Organelle Genomes
  • Organelle Genome Sequencing Program
  • Denmark

    Finland

  • Download plasmid drawing program Plasmid processor v 102
  • France

  • Nimes: Ecole pour les Etudes et la Recherche en Informatique et Electronique
  • Paris
  • CEPH-Généthon Fondation Jean Dausset
  • CEPH-Généthon Fondation Jean Dausset: integrated map
  • Généthon
  •  Pasteur Institute 'BioNetbook' searchable database of urls regarding biology (a web biology notebook), containing more than 3000 urls, classified according to 1. Resource Type, 2. Species or Organism, & 3. Discipline.
  • Germany

  • Berlin
  • Reference Library Data Base (RLDB) Hans Lehrach's Reference Library System
  • Resource Centre/Primary Database (RZPD) of the German Human Genome Project (DHGP) Replaces RLDB
  • Braunschweig
  • Molecular Bioinformatics of Gene Regulation DNA sequence features of regulatory genomic elements and regions, in particular those that govern transcriptional control and includes the TRANSFAC Database Release 3.0
  • Dusseldorf
  • PEDRO's BioMolecular Research Tools
  • Heidelberg
  • Integrated Genome Database (IGD)
  • EMBL
  • Predict protein server, protein secondary structure service
  • Starting places for Molecular Biology searching on Thure Etzold's SRS server
  • DSSP database of protein secondary structure assignments
  • Jena
  • Institut fur Molekulare Biotechnologie. Includes an 'Image Library of Biological Macromolecules' and the `RNA World'
  • Institut fur Molekulare Biotechnologie. Genome analysis group Includes GCG access and custom software such as 'Genetic Data Environment'.
  • Munich
  • Institute for Cell Biology
  • Holland

  • Amsterdam
  • 'Gene-Combis' molecular biology journal, Elsevier
  • Israel

  • Jerusalem
  • Weizmann Institute HotMolecBase, a collection of biomedically interesting molecules like p53, prion protein, huntingtin, presenilin- 1, and others. The entries for those molecules cover details about their cellular and molecular biology that cannot be found somewhere else on the web in this concentrated form. Their involvement in diseases, together with medical applications (progress in diagnosis and treatment), is also included.
  • Israel Science and Technology Israel's national database and directory of science and technology related web sites. It includes companies, government agencies, institutes of higher education, research centers, funds, associations, and conferences in Israel.
  • Japan

  • gopher to Japanese Biological Resources (JFCC & JTCA)
  • Kyoto: 'GenomeNet' Molecular Biology WWW Server
  • National Institute of Genetics, Japan
  • Norway

  • EMBnet sites (Map)
  • Sweden

  • 'Webcutter', restriction mapping of nucleotide sequences on line
  • Switzerland

  • Swiss Federal Institute of Technology Peptide and Nucleotide Analysis
  • Geneva: ExPASy molecular biology service. Analysis of protein and nucleic acid sequences as well as 2-D PAGE. It includes a facility to use the NiceProt view, see examples for SWISS-PROTPROSITESWISS-2DPAGE, SWISS-3DIMAGE, ENZYME and SeqAnalRef.
  • Interface to the EPFL-BLAST Network Service
  • SEQANALREF Sequence analysis bibliographic reference database, Switzerland.
  • Geneva Biomedical Research Institute Download Swiss-PdbViewer v 2.5.
  • MolMol MOLecule analysis and MOLecule display, molecular viewer
  • Crystallography resources world-wide Links
  • ISREC (the Swiss Institute for Experimental Cancer Research) since 1991 ISREC has had a research group in bio-informatics. Its main interest is in the detection and assessment of similarity between distantly related protein and DNA sequences by means of 'Generalized Profiles'. It also maintains EPD, the Eukaryotic Promoter Database, and the profile-based part of PROSITE, a catalogue of protein sequence motifs.
  • UK

  • DSC Protein Secondary Structure Prediction Given a single sequence, a multiple sequence alignment will be formed and DSC used to predict secondary structure, or given a multiple sequence alignment. DSC will use this alignment to predict secondary structure. DSC has a prediction accuracy of 70.1% on a standard set of 126 proteins. This was not significantly different from PHD, a popular prediction method. For medium length sequences DSC was more accurate than PHD, and combining DSC and PHD produced a prediction method more accurate than either.
  • Cambridge.
  • Genetics Library, Department of Genetics
  • MRC Laboratory of Molecular Biology
  • MRC Centre for Protein Engineering. It includes the 'Frontiers of Protein Structure Prediction' course.
  • NHS Public Health Genetics Unit. News and information about advances in genetics and their impact on public health and the prevention of disease.
  • Daresbury
  • gopher to the European Molecular Biology Network 'EMBNet'
  • EMBnet news
  • SEQNET National Database & EMBnet node WWW-services provided by SEQNET
  • Hinxton
  • MRC Human Genome Mapping ProjectHGMP.
  • GDB Genome Data Base mirror at HGMP. Download the Windows 3.1 or Windows 95 Version of 'Mapview' to study and select known regions and genes.
  • European Bioinformatics Institute (EBI)
  • European Biotechnology Institute ftp server of molecular biology software for all platforms
  • BIOCAT 4.1 software resources list, European Bioinformatics Institute, Cambridge
  • European Bioinformatics Institute: documentation, software and services
  • European Bioinformatics Institute, Geoff Barton's group and 'Protein Sequence Alignment and Database Scanning' manual.
  • European Bioinformatics Institute: Primers database, EBI
  • Protein DataBase PDB mirror site at EBI
  • European Bioinformatics Institute: Network browser for databanks in molecular biology
  • Genome-MOT web site monitoring the progress of genome sequencing projects
  • 'Fugu' comparative mapping project. Funded by the MRC to allow Sydney Brenner and Greg Elgar, through the HGMP, to generate a Landmark map of the puffer fish, Fugu rubripes (Fugu) genome.
  • Human Genome Mapping Project Resource Centre (HGMPRC)
  • Sanger Centresoftwareprojectsteams.
  • London:
  • Welcome Trust human genome website
  • Imperial Cancer Research Fund, PREPI (Protein Representations Interactively) molecular graphics viewer for IRIX
  • Galton Laboratory, University College
  • email HUGO's European general office
  • HUGO gene Nomenclature Committee Galton Laboratory, University College.Genes in GDB are designated by "approved" symbols. This Committee decides what they will be.
  • Sequence analysis facilities and information. molecular biology on-line publications, etc., Imperial College
  • 'Principles of Protein structure' Course early 1995, Birkbeck College
  • National Institute for Medical Research, Medical Research Council
  • University College: CINEMA - Colour INteractive Editor for Multiple Alignments. Java program for multiple alignment of protein or nucleic acid sequences.
  • Southampton
  • Location Database (ldb). An analytical database for constructing fully integrated genetic and physical maps.
  • 'Journal of Molecular Biology' This week's issue and this week's accepted papers. (Later registration necessary)
  • USA

  • Block Maker, The BLOCK MAKER SERVER finds blocks in a group of related protein sequences. Blocks are short multiply aligned unmapped segments corresponding to the most highly conserved regions of proteins. Typically, a group of proteins has more than one region in common and their relationship is represented as a series of blocks separated by unaligned regions.
  • The MEME System: Multiple EM for Motif Elicitation. MEME is a tool for discovering motifs in a group of related DNA or protein sequences.A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of DNA or protein sequences (the training set) and outputs as many motifs as requested. MEME uses statistical modelling techniques to automatically choose the best width and description for each motif.
  • Baylor: Sequence Annotation Server Maintained at Baylor College of Medicine. Molecular Biology Computational resource.
  • Baylor: Chromosome 8 Workshop
  • Baltimore
  • GDB: Genome Data Base GDB supports biomedical research, clinical medicine and professional and scientific education by providing storage and dissemination of data about genes and other DNA markers, map location, genetic disease and locus information. and bibliographic information.
  • GDB Genome Data Base mirror in UK at HGMP. You may use 'Mapview' to study and select known regions and genes. Downloadthe Windows 3.1 or Windows 95 Version of 'Mapview'
  • Clickable map of the human chromosome
  • gopher to the European Culture Collection Centre (ECACC)
  • The Johns Hopkins University BioInformatics Web Server
  • REBASE restriction enzyme database
  • Bar Harbor
  • Mouse Genome Informatics Project, Jackson Laboratory
  • Berkeley
  • LBL Lawrence Berkeley National Laboratory Human Genome Centre Information on HGC projects, Syndb Online LBNL Human/Mouse ACEDB-style Database.Drosophila physical mapping, etc.
  • LLNL Lawrence Livermore National Laboratory's Human Genome Center (LLNL)
  • Bethesda
  • gopher access to the American Type Culture Collection (ATCC)
  • WWW access to the American Tissue Culture Collection (ATCC)
  • National Library of Medicine 'HyperDOC', a Multimedia/Hypertext Resource.
  • Genome map at National Library of Medicine NCBI
  • 'NCHGR' National Center for Human Genome Research. This is a general introduction to the programs of the National Center for Human Genome Research.The 'NCHGR DER' is the component of the National Institutes of Health with responsibility for the Human Genome Project.
  • NCBI (NIH's 'National Center for Biotechnology Information') has outstanding resources for the general public and scientists: 'Human Genome Resources'. 'NCBI News'; dbEST and GenBank'BankIt' DNA sequences submissions to GenBank'Entrez..', 'BLAST', 'Bankit', 'OMIM', taxonomy and structure searching'Entrez' DatabaseSearch 'Entrez..'; Online Mendelian Inheritance in Man (OMIM)with links to the 'Entrez' database of MEDLINE articles and sequence information. 'Entrez Genomes Views' has current data on sequenced DNA; data on the malaria genome; 'IgBLAST' human and mouse immunoglobulin data. 
  • NCGR National Center for Genome Resources, Genome Sequence Data Base (GSDB)
  • BIOSCI: Bionet Newsgroups
  • 'bio101': plasmid purification kit home page
  • Boston
  • MGH Neurogenetics homepage Information on a variety of neurogenetic diseases including neurofibromatosis type I (Von Recklinghausen's disease) and 11, tuberous sclerosis and Von Hippel-Lindau disease
  • Links to information on how to use molecular biology databases
  • Brookhaven
  • Brookhaven National Laboratory
  • Genome sequencing facility, Brookhaven National Laboratory
  • Cambridge
  • Biology biopages WWW Resource
  • World-Wide Web Virtual Library. Biochemistry, Biophysics and Molecular Biology. Information categorized first by provider, then by subject
  • Harvard Biolabs home page
  • 'Flybase'
  • Whitehead Institute for Biomedical Research/MIT Center for Genome Research
  • DOE: Human Genome Program, Health Effects and Life Sciences Research Division, Department of Energy.
  • EMBNET: BIOSCI/Bionet Newsgroup Archives
  • Emory: Molecular Biology and Medicine, Emory University
  • Emory: MITOMAP: A database of the "Report of the committee on human mitochondrial DNA", Emory University
  • 'Genome Channel'. A series of interface tools for visualization and querying the reference human genome and other genomes assembled and annotated by the Genome Annotation Consortium (GCA). 'Genome Channel' User's Guide.
  • Human Genetics Education Resource listings at AspiringNurse.
  • Illinois: ftp the Ribosomal Database Project, UIUC Illinois
  • Indiana: PEDRO's BioMolecular Research Tools
  • Iowa: Cooperative Human Linkage Center (CHLC) The goal of the Cooperative Human Linkage Center is to develop statistically rigorous, high heterozygosity genetic maps of the human genome that are greatly enriched for the presence of easy-to-use PCR-formatted microsatellite markers.
  • Los Alamos: LANL Los Alamos National Laboratory Centre for Human Genome Studies
  • Los Alamos: LANL Human Genome Most Used Links Mapping data sites, access to YAC search pages, Baylor.
  • Maryland: Agricultural Genome Information Server
  • Michigan: Human Genome Center
  • New York
  • Rockefeller University
  • Skirball Institute of Biomolecular Medicine, NYU
  • molecular biology & amp; protein databases, Cold Spring Harbor Laboratory
  • 'MathMol' Molecular modelling and visualization, NYU
  • Cold Spring Harbor Laboratories Manual Source Book product/supplier database In the search engine just type in oligonucleotide synthesis, and a comprehensive list of suppliers will appear along with their phone numbers. Complete contact information can also be found for more than 1400 suppliers
  • 'Genome Analysis', a book series edited by Kay Davies (Vols 1-5) and Shirley M. Tilghman Vols 6 and 7), Cold Spring Harbor Laboratory
  • ORNL: Human Genome Management Information Systems (HGMIS) Information on US DOE Human Genome Project.
  • Philadelphia: Nucleic Acid/Protein Research Core Facility, Children's Hospital of Philadelphia
  • PREMIER Biosoft  bioinformatics company based in Palo Alto.
  • Protein Data Bank, PDB. The Rutgers State University of New Jersey.
  • Research Genetics
  • San Diego
  • Biomedical Informatics Research Network (BIRN) at the San Diego Supercomputer Center (SDSC)
  • Stanford
  • Saccharomyces Genome Database, Stanford University
  • St. Louis
  • Washington University DNA/GUI gel analysis program St. Louis, Washington University
  • Download DNA/GUI gel analysis program
  • TIGR
  • UTHSCSA: Chaperonins GroEL/GroES mutation databases and a Chaperonin structure gallery.
  • UWF: gopher: Methods: DNA cloning in E. coli, Univ. East Florida
  • UIC: ftp: Download 'tacg', a command line tool for the restriction enzyme analysis of DNA
  • Virginia: ftp: 'fasta'
  • Seattle
  • 'Phylip' software home page, Joe Felsensten
  • Other resources

    Genomics.com Molecular biology and biochemistry software resources.
    'Nature' 'Genome Gateway' including links to genomics sites.

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