BPS 4104 Lecture Notes - Lecture 9: Pyrimidine, Deamination, Phylogenetics
27 Mar 2018
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We know 2 scoring mechs: constant gap penalty and other . Blast = go =5; ge = 2; match = 3; mm = -1. S = transitions, occurs very frequently, don"t take many pts off. V = transversions, take many points off bc don"t occur as often. 2 sequences randomly generated, twice as many transversions than transitions. Not the normal genetic code, trp coded instead of stop codon. Transitions are synonymous and transversions are nonsynonymous at two-fold degenerate sites. G/u pair, although not as strong as a/u or c/g pair, generally does not disrupt rna secondary structure (and occurs frequently in rna secondary structure). I often say that when you can measure what you are speaking about, and express it in numbers, Coevolution, r. e means methyltransferase that recognizes the same site and modifies it so that not recognized by r. e so it knows foreign or non-foreign dna. Deacetylases: an enzyme that removes an acetyl group.
