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Determine sequence weights

Determine sequence weights for the sequences ACTA, ACTT, CGTT, and AGAT in problem 1 by using Thompson, Higgins, and Gibson method

a) compute pairwise distances between sequences

b) build phylogenetic the tree using UPGMA method 

c) derive sequence weights 

Problem 2

We assumed additive property when constructed UPGMA tree  in problem 1.

What is limitation of this assumption?

Problem 3

The sequence of gene "B3" was used to blast against swissprot protein database. The query returned five significant hits to other proteins denoted by B1,B2,B4, B5, and H in the figure below. B1-B5 are five bacterial species, while the species H represents Homo sapiens. No other mammalian species have shown presence of protein that is similar to B3. Explain the presence of this gene in humans.

851_sequence-weight.png

 

Problem 4

Describe technical and theoretical challenges associated with building phylogenetic trees.

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