Harvard:Biophysics 101/2007/Notebook:Kaull/2007-2-20

My project - still alpha, heh - is an attempt to evaluate the selective pressures on synonymous codon frequency in ApoE.

There was some discussion earlier in this course about synonymous codons and their distribution; some call codon distribution a random process, biased by co-evolution between tRNA and codon levels, while others say that rare codons may be an advantage at some sites (such as domain boundaries). If the abundance or scarcity of a codon is an advantage, it should be conserved - if it is random, it should not be. Thus, my project.

GenBank says that ApoE is directly conserved in eutherian mammals, so I'm using chimp, dog, rat and mouse ApoE as comparison samples for the human version. I aligned them with Clustalw, compared the codons at each aligned site, and I'm now playing with the data to see if anything interesting falls out. Will report back in a bit.

PS: Big thanks to the TAs for helping me teach Python and Clustalw to get along.