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|BioInformatics Courses and Tutorials
- UCL's Web practical on bioinformatics with online
examples and practicals. An excellent training and teaching resource on protein
sequence and structure analysis: A practical guide "A taste of
bioinformatics". Visit the UCL site describing
the structure and composition (with hyperlinks) of EMBNET,
the European Molecular Biology Network. Contents also includes the US Bioinformatics
network and sites. See also:
Structure Course - at Birkbeck College London
(See separate entry in Protein Page). This is the
entrance site for the index of contents and entry to textual information for the course
"The Principles of Protein Structure '97" .
Coursebook - a set of tutorial texts developed for the award-winning
VSNS-BCD BioComputing Courses, aimed at a mixed audience of biologists, computer
scientists, and students + researchers of related areas, on a late undergraduate /
BIOcomputing Tutorials - On-line tutorials on
various aspects of database searching from the CAOS/CAMM Center at Nijmegen University.
See the list of tutorials available; BIOcomputing section most relevant. For those who
have access to the World Wide Web, the Center offers a growing number of Interactive
Tutorials. Currently courses have been developed or are under construction for a number of
CAMMSA topics, for some CAMM topics and for some CAOS topics.
The goals of the BioLib project are to acquire, access
and develop JAVA-based bioinformatics tools which are robust, easy to use and
interoperable and to construct a unique bioinformatics library (BioLib)
which will help scientists extend and customize their software capabilities. The project,
is a joint project of Oxford Molecular, Astra Bioinformatics Centre (Sweden), Glaxo
Wellcome and Silicon Graphics, and in conjunction with Nottingham University, Trinity
College Dublin, and Åko Akademi University. venture partially funded by the UK Department
of Trade and Industry and Finnish Technology Development Center (TEKES).
Data and software provided mainly includes genome mapping
information, tools and maps:
A physical gene map of the human genome
Graphical interface to public genome maps
Links to other Bioinformatics Sites
Chromosome-specific web sites
Oxford Molecular Home
page in UK
BioShow UK is a shopwindow of UK bioinformatics
resources. It aims to be a central information point on software, databases, WWW-,
ftp- and E-mail services produced/available in the UK. All information is stored in a
database which is fully integrated in the SEQNET SRS server. Authors/maintainers of
bioinformatics resources are invited to deposit information about their work. It is also
possible to make databases and software available on the BioShoW UK FTP server.
- The BioToolKit locates online molecular biology research tools
for the analysis of nucleic acid and protein sequences, genome structure, and
biomacromolecular structure and function. Features an internet directory of 500 key
research resources for molecular biologists, now hosted by BioSupplyNet. The whole collection of
resources or each specific set of tools (Nucleic Acid Analysis, Genome Resources or
Protein Structural Imaging and Analysis) is searchable.
- CLUE is a large collection of convenient links where various
URLs from different areas of genetic research are contained. Select from the
list provided for a simple search, or go to advanced search where you can search for URLs
by entering keywords. Provides a comprehensive categorised set of links to most WWW
molecular biology sites and servers.
- The Dali server is a network service for comparing protein
structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein
Data Bank. A multiple alignment of structural neighbours is mailed back to you. In
favourable cases, comparing 3D structures may reveal biologically interesting similarities
that are not detectable by comparing sequences. If you want to know the structural
neighbours of a protein already in the Protein Data Bank, you can find them in the FSSP database. For more details and help try DALI HELP.
Home page of the DNA Data Bank of Japan at the Center
for Information Biology, National Institute of Genetics, Mishima, Japan. DDBJ is the sole DNA data bank in
Japan, which is officially certified to collect DNA sequences from researchers and to
issue accession numbers to data submitters. We collect data mainly from Japanese
researchers, but of course accept data and issue accession numbers to researchers in any
other countries. We exchange the collected data with EMBL/EBI
and GenBank/NCBI on daily base, so that the data banks share
virtually the same data at any given time. We provide any researcher with WWW, anonymous
ftp service, e-mail servers, and Gopher server through which they may access our database.
Contact address: National Institute of Genetics, 1111 Yata, Mishima, 411 Japan, E-mail
address for inquiries: email@example.com
Numerous bioinformatics software packages are available free over the network but
each has its own method of interaction and data format. There are several commercially
available packages that amalgamate a programmes and use a common method of interaction and
data format. There are few free packages that do a similar thing. DISguISE
was developed with this aim in mind. In effect, to `disguise' the underlying programmes
and data with a general graphical user interface that hides any implementation details.
DISguISE has been written using
tcl/tk a freely available and easy to use interpreted tool command language and X windows toolkit. Each programme is included as a separate tool,
with each tool having a common look and feel. A single data format is used for transfer of
data between tools. The common look and feel is determined by core code which also
provides procedures for other common tasks. This common code has the added advantage that
it minimises the effort required to include programmes. Many of the programmes available
in the gcg package are available through the DISguISE interface as well as many others that are available on
the SEQNET. The programmes available range from database
searches, retrieving sequences from the databases, includes sequence alignments, through
to structure prediction and analysis of sequences. DISguISE
can handle DNA/RNA as well as protein sequence data. There is also front end interfaces to
mail servers and WWW pages that offer bioinformatic services. Utilities like a file
browser and a multiple alignment sequence editor are available within the DISguISE client.
This is the World-Wide Web (WWW) server of the European Bioinformatics
Institute (EBI) which is located at Hinxton Hall, near
Cambridge in the United Kingdom. The EBI is an Outstation of EMBL on the Wellcome Trust Genome Campus, Cambridge, UK.
Gateway to Services with
links to various EBI and other databases, FTP archives,
searching tools, data submission, on-line applications and querying databases or Research with links to genequiz, protein
structure and folding, protein topology, genome projects, mutation.
Index - Gavin Thompsons E.coli compendium site at
University of Birmingham. These pages contain a comprehensive guide to information
relating to the bacterium Escherichia coli on the WWW. Links to numerous
databases including: E.coli genome projects, E.coli databank, transport
proteins, E.coli proteomics page (N-terminal sequences from 2D gels), strain and
genotype lists, E.coli genetic stock centre, codon usage, EcoCyc-genes and
metabolism encyclopedia (see separate entry in enzyme corner
- The World Wide Web server at EMBL, the
European Molecular Biology Laboratory - comprising of the main laboratory at Heidelberg
and 3 Outstations at Grenoble, Hamburg and Cambridge (EBI, see separate entry). This site provides
detailed listings and links to software, services and information for sequence
manipulation and searching. More information on EMBL can be found on the home page.
EMBNET - The
European Molecular Biology Network. The EMBnet brochure contains information about the membership and the
structure of the organisation. It exists as an electronic publication which you can access
from EMBnet. EMBnet
also publishes a newsletter, EMBnews
devoted to provide information about what is happening at the national and special nodes.
This publication contains articles on software and database development, interviews, hints
and tips for EMBnet users as well as conference announcements
and activity reports.
- The Entrez Browser is provided by the National Center for
Biotechnology Information (NCBI). NCBI
also builds, maintains, and distributes the GenBank Sequence
ExPASy Molecular Biology
Server - This is the ExPASy
World Wide Web molecular biology server of the Swiss Institute of Bioinformatics (SIB)
maintained in collaboration with the Geneva University Hospital and the University of
Geneva. This server is dedicated to the analysis of protein sequences and structures as
well as 2-D PAGE. See other ExPASy entries in this table.
menu - extensive and useful collection of tools
on the ExPASy server for protein sequence identification and
Swiss-Shop - a sequence alerting system for SWISS-PROT that allows you to automatically obtain (by email) new sequence entries
relevant to your field(s) of interest. (See separate entry).
AACompIdent - Identify a protein by its amino
AACompSim - Compare the amino acid composition
of a SWISS-PROT entry with all
Identify proteins with pI, MW, amino acid compositon, sequence tag and peptide mass
GuessProt) - Get the SWISS-PROT
proteins closest to a given pI and Mw and identify proteins with a sequence tag.
FindMod - Predict
potential protein post-translational modifications and potential single amino acid
substitutions in peptides. Experimentally measured peptide masses are compared with the
theoretical peptides calculated from a specified SWISS-PROT entry or from a user-entered sequence, and mass differences are used to
better characterise the protein of interest.
Calculate masses of peptides and their posttranslational modifications for a SWISS-PROT or TREMBL entry or for a user sequence.
Compute pI/Mw - Compute
the theoretical pI and Mw from a SWISS-PROT or TREMBL entry or for a user sequence.
The site has hyperlinks to many other
protein characterisation sites.
Japanese WWW server. The GenomeNet services are operated jointly by the Supercomputer
Laboratory (SCL), the Institute for Chemical Research (ICR), Kyoto University and the Human Genome Center (HGC), Institute of Medical Science, the University of Tokyo.
- Useful site with a wide range of JAVA/Bioresources from within JMBW
pages (See separate entry). Links to software for a multitude of online sequence
manipulations - translation, restriction, sequence retrieval, RNA structure, pattern
searching, codon usage, oligo designers and genomic map viewers.
- Java-based Molecular Biologist's Workbench version 1.1.
The programs and documentation that you will find here have been put together in order to
try to give free access to the most common bioinformatic operations that a molecular
biologist currently requires. JaMBW does however take advantage of the foremost
developments in computer science in order to make it simple to use. The latter includes,
therefore, point-and-click, drag-and-drop, plug-and-play. Most of these requirements are
met by the use of Java programming language conformant to the JDK1.02 specifications.
JaMBW can be run on-line or can be downloaded to your own machine; above all it is free!
- Gateway to National Center for Biotechnology Information at Bethesda,
MD, home of GENBANK database. Links to a wide range of
database and search resources (see shorcuts below).
- Munich Information Centre for Protein Sequences MIPS is
located at the Max Planck Institute for Biochemistry, Munich. This is the bioinformatics
group of the GSF at the Max-Planck-Institut f. Biochemie contributing to the
PIR-International Protein Sequence Database the European Yeast Functional Analysis Program
(Eurofan) the European Sequencing of Arabidopsis thaliana (ESSA) the German Network for
Functional Analysis in Yeast the European Molecular Biology Network (EMBnet).
- BioMolecular Research Tools, this is one of the most comprehensive web
sites for bioinformatic databases and software. Includes in three sections: 1.
Molecular Biology Search and Analysis; 2. Bibliographic, Text and File Searches; 3.
Guides, Tutorials and Help Tools:
Southampton BioInformatics Data Server - useful front end access to sequence and
structural databases including: Submit a sequence to the EMBL database; Retrieve a
sequence or PDB structure file by accession number; Access sequence databases containing
DNA/RNA or protein; Access the various Genome projects; Analyse DNA and protein sequences;
Access databases containing structural information; Access Internet sources on Molecular
Biology, Protein modelling and crystallography, Biology, Bionet Newsgroups, Medicine etc.
This is the WWW home page for SEQNET the U.K. academic
communities SEQuence NETwork
computer for molecular biologists, funded by the BBSRC and the U.K. national node of the
European Molecular Biology Network (See separate entry). The SEQNET
central node at Daresbury offers access to all major molecular biology sequence and
structure databases and programs for UK academics. All major software packages are
provided (e.g. GCG, EGCG, Staden, Pearson fasta, Blast, Phylip)
plus a host of other utilities, particularly for protein analysis. Network services
include Internet NEWS, anonymous ftp and distribution of the EMBnet
and BIOSCI bulletin boards.
The SRS 5 Sequence Retrieval facility features one of
the largest collections of interlinked databases available for this system. SRS Sequence Retrieval System (version 5) is a World
Wide Web interface for the recovery of nucleotide and protein sequences from a wide range
of databases (list of more than 30 provided). Compared with other SRS
interfaces SRSWWW has more users because of the widespread
use of web browsers, its easiness to handle and its user friendly interface. This is a
relatively massive site with many links. Provides a relatively user-friendly
environment for sequence retrieval from many different databases. Several servers use SRS
system. There are several servers providing access to SRS - the link provided here
is to the SRSWWW server at EMBL-EBI, Hinxton, UK , version
5.1.0. Use this Enquiry
Form to start a search session. Full on-line manual available.
SWISS-PROT Gateway to
the SWISS-PROT Protein Sequence Data Bank. This is a database
of protein sequences produced collaboratively by Amos Bairoch (University of Geneva) and
the EBI. It contains high-quality annotation (such as the description of the function of a
protein, its domain structure, post-translational modifications, variants, etc), has a
minimal level of redundancy, is non-redundant, and cross-referenced to many other
databases. Release 35.0 (May ' 98) of SWISS-PROT contains
72923 sequence entries, comprising 25'083'768 amino acids abstracted from 59'101
references. SWISS-PROT is accompanied by TREMBL, a computer-annotated supplement to SWISS-PROT.
TREMBL contains the translations of all coding sequences
(CDS) present in the EMBL Nucleotide Sequence Database not yet integrated into SWISS-PROT. TREMBL can be considered as a preliminary section of SWISS-PROT as all TREMBL entries have been assigned SWISS-PROT accession numbers. TREMBL
is split into two main sections; SP-TREMBL and REM-TREMBL. SP-TREMBL (SWISS-PROT TREMBL) contains the entries which should eventually be
incorporated into SWISS-PROT. Release 5 of TREMBL is created from release 53 of the EMBL
nucleotide sequence database and contains 166,361 sequence entries, comprising 45,671,684
Yeast Database at MIPS (See separate entry for MIPS). This is
the European part of the Yeast Genome Project funded by the European Commission, under the
Biotechnology RTD Programs. From this page you can access (via menus) the annotated
sequence information of the genome of Saccharomyces cerevisiae. You may view the
chromosomes graphically or as text, use the Genome-Browser,
browse and search the proteins in the PIR-database and more.