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BI379_F09_Exercise_3 - Wherease Table 1 represents...

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BI379 F09 Assignment 3 Due Tuesday, Oct 6 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. 2. In Table 1, there is a column labeled “amino acid distance”. What does this represent and why are there 3 different values? Also, why is the first value always lower than the following two? 3. In your own words , tell me what source of systematic error they are concerned about (with respect to their analysis). 4. Table 2 represents the most complex analysis in the paper.
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Unformatted text preview: Wherease Table 1 represents interspecied comparisons (e.g. human vs chimp for hominidae), Table 2 incorporates polymorphisms found withing human genomes (SNPs), which are believed to be predominantly neutral (i.e. there is little to no positive selection for these intra species changes). Describe what the last column in Table 2 represents (Relationship between divergence and polymorphism) and what it allows them to conclude about interspecies changes. 5. In Table 3, they do a bit of speculation and show the current frequency of each amino acid and extrapolate where these frequencies are going in the distant future (asymptotic frequency). They also mention that “in extant proteins, gainers tend to be under-represented (except for Met) and losers are overrepresented (except for Pro)”. What two columns are they comparing in Table 3 to make this statement?...
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