Lecture 2 exercises
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- What is the “best” protein substitution matrix to use?
- Which amino acids are the least mutable according to the BLOSUM62 matrix?
- The most mutable?
- Most frequent mutation?
- Least frequent mutation?
- Is a hippopotamus more closely related to a pig or to a whale, based on the protein sequence of hemoglobin for each organism? Explain.
- The coelacanth Latimeria chalumnae is large fish that has been called a "living fossil." Long thought to be extinct for at least 90 million years, several specimens have now been discovered lurking in the ocean. Incredibly, some phylogenetic analyses of mitochondrial DNA sequences indicate that the coelacanth is more closely related to humans than to herrings (Lewin, 2001). Find the accession numbers for some mitochrondrial DNA from human, herring and coelacanth, and then perform pairwise alignments to decide if you agree. Hint: the genus and species of herring is Clupea harengus. Search Entrez such as "Clupea harengus mitochondrion".
