Links to
Molecular
Biology resources
This page was written
by Christopher Spry.
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 email Christopher 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
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
Human
CpG Island database
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-PROT, PROSITE, SWISS-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 Project, HGMP.
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
Centre, software, projects, teams.
London:
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. Download the
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
progams 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' Database;
Search
'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.
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
Protein Data
Bank, PDB. The Rutgers State University of New Jersey.
Research
Genetics
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
Genomics.com
Molecular biology and biochemistry software resources.
'Nature' 'Genome Gateway'
including links
to genomics sites.
Go to the 'home
page'
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© cspry@sghms.ac.uk.
Department of Biochemistry & Immunology, St. George's Hospital Medical
School, London SW17 0RE, UK. Phone +44 20-8725 5819; fax +44 20-8725 5821.
This page was last updated on
23 May 2002 15:34:50.