Bioinformatics - Exam

1. Consider the following proteins from UniProtKB:

 P04655
 P04654
 P47710
 P08949
 P47851

a) Determine the families to which these proteins belong by using an appropriate tool.
Describe the consensus patterns of these families.

b) For each detected family, construct a multiple sequence alignment for the proteins belonging to the family. Find highly conserved regions in the proteins under consideration by examining the multiple sequence alignments. Are the consensus patterns of the families correctly reflected in the alignments?

c) Use a corresponding tool to provide a phylogenetic tree for the five proteins.
Does the tree reflect the family relationship correctly?

2. Consider the fibrinogen-binding protein from Staphylococcus aureus (accession P68799). Determine the secondary structure by a method of your choice.  Compare the predicted secondary structure for the given protein with the real one.

3. Basic Questions:
a) Explain the difference between standard Monte Carlo method and importance sampling.

b) How many genes has the HI virus?
 Which genes are not present in the human genome?

c) Given a phylogenetic tree with character data at the leaves:

            /\
           /  \
          /\  /\
        GCCA

Find the most parsimonious tree using Fitch's method.

d) What is an additive tree?