Bethe Ansatz in the Bernoulli Matching Model of Random Sequence Alignment

Satya N. Majumdar 1, Kirone Mallick 2, Sergei K. Nechaev 1

Physical Review E: Statistical, Nonlinear, and Soft Matter Physics 77 (2008) 011110

For the Bernoulli Matching model of sequence alignment problem we apply the Bethe ansatz technique via an exact mapping to the 5-vertex model on a square lattice. Considering the terrace-like representation of the sequence alignment problem, we reproduce by the Bethe ansatz the results for the averaged length of the Longest Common Subsequence in Bernoulli approximation. In addition, we compute the average number of nucleation centers of the terraces.

  • 1. Laboratoire de Physique Théorique et Modèles Statistiques (LPTMS),
    CNRS : UMR8626 – Université Paris XI - Paris Sud
  • 2. Service de Physique Théorique (SPhT),
    CNRS : URA2306 – CEA : DSM/SPHT