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In the tutorial in the appendix a short introduction to programming including install­

ing BLAST or in general a web server is given. Generally speaking, web-based pro­

grams and good bioinformatics algorithms and scripts for bioinformatics analysis are

still developing rapidly and there are many fascinating programming tasks. ◄

6.3

Exercises for Chap. 6

You are welcome to work on the tasks of Chap. 1 for this chapter as well.

Task 6.1

A simple illustration: How do you look something up in a book? Discuss different

approaches.

Task 6.2

Comparison “fast” and “super fast”: How do BLAST, FASTA and Psi-BLAST differ in

terms of their search strategy?

Task 6.3(a)

What is BLAT (not a typo, bioinformatics question)?

Task 6.3(b)

What are the advantages of BLAST as sequence comparison tool?

Task 6.4

Which sequence comparison search is fastest? Give some examples and consider which is

the very fastest. Compare the advantages and disadvantages.

Task 6.5

Which annotation is best? Compare: Annotations in GenBank, UCSC Genome Browser

and Swiss-Prot/UniProt.

Task 6.6

In your opinion, how should an “ideal” database/server be constructed (what basic parts

should the database/server consist of)?

Task 6.7

List ways in which ideally a database should be maintained and kept up to date.

6.3  Exercises for Chap. 6