Thursday, April 7, 2011 - 15:05
1 hour (actually 50 minutes)
We consider two random sequences of equal length n and the alignments with gaps corresponding to their Longest Common Subsequences. These alignments are called optimal alignments. What are the properties of these alignments? What are the proportion of different aligned letter pairs? Are there concentration of measure properties for these proportions? We will see that the convex geometry of the asymptotic limit set of empirical distributions seen along alignments can determine the answer to the above questions.