Fluctuation of the Optimal Alignment Score via Monte Carlo

Research Horizons Seminar
Wednesday, December 5, 2012 - 12:05
1 hour (actually 50 minutes)
Skiles 005
Georgia Tech, School of Math
The question of the asymptotic order of magnitude of the fluctuation of the Optimal Alignment Score of two random sequences of length n has been open for decades. We prove a relation between that order and the limit of the rescaled optimal alignment score considered as a function of the substitution matrix. This allows us to determine the asymptotic order of the fluctuation for many realistic situations up to a high confidence level.