An O(n log n)-time algorithm for the restriction scaffold assignment problem

J Comput Biol. 2006 May;13(4):979-89. doi: 10.1089/cmb.2006.13.979.


The restriction scaffold assignment problem takes as input two finite point sets S and T (with S containing more points than T ) and establishes a correspondence between points in S and points in T , such that each point in S maps to exactly one point in T and each point in T maps to at least one point in S. An algorithm is presented that finds a minimum-cost solution for this problem in O(n log n) time, provided that the points in S and T are restricted to lie on a line and the cost function delta is the L(1) metric. This algorithm runs in linear time, if S and T are presorted. This improves the previously best-known O(n (2))-time algorithm for this problem.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Computational Biology*
  • Data Interpretation, Statistical
  • Linear Models