1) On the following tree, identify the total number of gene
duplication events and label the nodes that correspond to gene
duplication events.  Assuming both the human and gorilla genomes are
complete and the entire gene set is known, what is the minimum number
of gene loss events that can explain this tree (3p)?

human 1--|
         |--|
human 2--|  |
            |--|
human 3-----|  |
               |--|
gorilla 1--|   |  |
           |---|  |--
gorilla 2--|      |
                  |
human 4-----------|


2) Varför fungerar vanliga sekundärstruktursprediktionsprogram dåligt för
integrala membranproteiner? (3p)


4) Give two examples of differences in the organisation of genes in the
genome of a eukaryote compared to a prokaryote. (3p)


5) One step in identifying the location of a gene in a genomic
sequence is to find an Open Reading Frame (ORF). What is an ORF? Give
two reasons why it is usually necessary to use additional criteria to
identify a gene in a eukaryotic genome sequence. (3p)


6) Assume that you have been given a nucleotide sequence about which very
little is known. Which of the following databases would you use to
search for information about it, and why (3p)? 
a) EMBL
b) SwissProt
c) Protein Data Bank (PDB)


7) How is PSI-BLAST used in protein structure prediction and modelling methods?
Describe one important situation where PSI-BLAST cannot help you. (3p)

8) Why are E-values usefull. What do they desribe ? How are they
  calculated in blast and in fasta ? (3p)


9) What is the differnce in the dynamic programming algorithm between
  local and global alignments ? (3p)


10) Why are mostly local alignments used for database searches ? (3p)