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The purpose of this practical is to introduce a range of bioinformatics services, databases
and software available on the Web and to illustrate their advantages and disadvantages.
The practical consists of
three tutorials, each comprising several Chapters.
The
Basic tutorial deals with DNA translation, similarity searching of protein sequence and
family databases, sequence alignment, protein structure classification and tools for secondary structure
prediction. The Advanced tutorial
builds on these approaches, introducing more advanced techniques of homology modelling and fold recognition.
Finally, the
Case studies provide an opportunity to apply
all of these techniques - and new ones - to credible biological problems.
The interface is structured as follows:
- on the left, a table of contents details the Chapters - the current Chapter is highlighted
- on the right, a header contains the current Chapter title and navigation tabs - clicking on these
allows access to the contents as outlined below:
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Navigation
tab |
Content |
Present
in all Chapters? |
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A brief outline of the Chapter's goals |
y |
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A series of Steps describing what you need to do and links to follow, featuring:
- Previous and Next buttons to navigate through the Steps
- Reflections... to help you think more deeply about the Steps
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y |
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An introduction to the principles behind the techniques used, featuring:
- illustrative images and animations
- links to other Websites with further information
|
n
(short popup information boxes may be provided instead)
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A self-assessment exercise, featuring:
- a set of multiple
choice questions
- an assessment
of your performance
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n |
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Bibliographic references:
- ordered by author
- with MEDLINE links
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At the end of the practical are Final assessment
and Appendix sections. The former contains a Final quiz,
to help you assess what you have learned; it also contains a Feedback
section with a questionnaire and a contact us form, to help us make improvements. In
the Appendix is a Glossary of bioinformatics-related terms and a Contributors page.
Always
- Keep in mind a Chapter's aims.
- In the instructions,
- Read NOTEs in each Step carefully.
- Keep accession numbers, sequences and any other important results using the Notepad provided (remember to save your results - the Notepad will not keep data between sessions).
- If the services are slow, do make use of the alternative links provided.
- In the Reflections...
- take time to answer all the questions.
- Follow the HINTs to help find an answer.
- As before, note your answers.
- In the info,
follow links to online documentation - they help you understand important principles and to answer questions.
- Repeat the quiz until you get the questions right.
The Web is a dynamic environment, where information is constantly added and removed.
Servers "go down", links change without warning, databases change their data structures and
formats, scripts of on-line services change, connections
to distant servers can be slow, etc. This can lead
to "broken" links, unexplained missing pages, results not being returned from services.
Don't give up - give it a second go. If nothing works, try a search
engine, using terms related to the service or to the page you are trying to access.
Please use the Feedback section to help us maintain and improve the site.
When ready, proceed to Chapter 1, and good luck!
The EMBER Team
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