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(processing or calculation part; of course, you have to have created the reference database

first), and finally there is a nice output list (list of hits and statistical parameters).

Question 1.6

Answer A, C, D

Example 1.7

Answer B.

The BLAST algorithm can perform a number of searches, e.g. blastn for a nucleotide

sequence and blastp for a protein sequence. But it can do much more, e.g. blastx translates

a nucleotide sequence into a protein sequence and then searches against the protein data­

base, tblastn searches with a protein sequence against a translated nucleotide database, and

tblastx searches with a translated nucleotide sequence against a translated nucleotide

database.

Example 1.8

Answer A, D.

The sequence comparison with BLAST first tells what the function of the sequence is

(which piece of which virus is here as a sequence). In the example, the blastp search

should have found the pol protein and protease of HIV-1. Another important output is the

E-value (expected value). This indicates that my output alignment will be found again in

the database with a similar or better score, so it depends on the size of the database (unlike

the p-value). If you are looking for the highest possible similarity, the selected BLAST hit

should have the smallest possible e-value and a high identity.

20.1

Question 1.9 and Example 1.10

A dotplot allows you to compare two sequences on a graph (x−/y-axis) to find similar

areas (represented as a dot). In both cases (by hand and software), your dotplot should find

similar areas between the two exercise sequences.

20.2

Magic RNA

Example 2.1

1. Answer C, E

20.2  Magic RNA