Exact solution of the Bernoulli matching model of sequence alignment

V B Priezzhev, G.M Schütz
2008 Journal of Statistical Mechanics: Theory and Experiment  
Through a series of exact mappings we reinterpret the Bernoulli model of sequence alignment in terms of the discrete-time totally asymmetric exclusion process with backward sequential update and step function initial condition. Using earlier results from the Bethe ansatz we obtain analytically the exact distribution of the length of the longest common subsequence of two sequences of finite lengths $X,Y$. Asymptotic analysis adapted from random matrix theory allows us to derive the thermodynamic
more » ... e the thermodynamic limit directly from the finite-size result.
doi:10.1088/1742-5468/2008/09/p09007 fatcat:7vkbxrzbqzba7ofxpcjfweqhu4