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BI379_F09_Exercise_3_key - BI379 F09 Assignment 3 Key...

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BI379 F09 Assignment 3 Key Answer the following questions about the paper entitled “A Universal trend of amino acid gain and loss in protein evolution” (Jordan et al., Nature, Feb 2005, Vol 433, pp 633-638.) Don’t forget that the results of this paper are also discussed in your text. 1. The paper is looking at amino acid changes in orthologous genes in various taxa by using three- way alignments. Describe the three-way alignment and tell me why this was used (as opposed to a two-way alignment. Three way alignments involve an alignment of the three different sequences (I know… duh!). In this case, they are comparing the sequences of a given ortholog from three distinct specie – two that are closely related (sister species) and one that is more distant (the outgroup). In this matter, they can determine in some cases what the ancestral amino acid at a given position is by noting cases where the outgroup matches one of the sisters. If the other sister contains a different amino acid, that change can be used for the study. With a
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