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Table 3 Employing an algorithm for the LCP problem to solve the MAD problem

From: The difficulty of protein structure alignment under the RMSD

Input: sequences P = (p1,…,p n ), Q = (q1,…,q m ) and I.
  Without loss of generality assume m ≥ n.
Output: (i) subsequences PP, QQ, |P| = |Q|, and
  (ii) mapping f:PQ, fulfilling the following conditions:
  (A) |P| = ,
  (B) d = RMSD(P,f(p)) is minimized.
1. l ← 0, u ←  c max
2. m ← 1/2(l + u)
3. Call LCP to solve the instance (P,Q,m).
4. If the LCP solution has size no less than
  u ← m
  else
  l ← m
5. If u-l 12 c max 2 - 12 c max 2 - 1 2 ,
  Output the most recent LCP solution of size no less than .
  Otherwise, repeat Steps 2-5.