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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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