Combinatorica

, Volume 26, Issue 2, pp 141–167 | Cite as

On The Parameterized Intractability Of Motif Search Problems*

  • Michael R. Fellows
  • Jens Gramm†
  • Rolf Niedermeier‡
Original Paper

We show that Closest Substring, one of the most important problems in the field of consensus string analysis, is W[1]-hard when parameterized by the number k of input strings (and remains so, even over a binary alphabet). This is done by giving a “strongly structure-preserving” reduction from the graph problem Clique to Closest Substring. This problem is therefore unlikely to be solvable in time O(f(k)•nc) for any function f of k and constant c independent of k, i.e., the combinatorial explosion seemingly inherent to this NP-hard problem cannot be restricted to parameter k. The problem can therefore be expected to be intractable, in any practical sense, for k ≥ 3. Our result supports the intuition that Closest Substring is computationally much harder than the special case of Closest String, althoughb othp roblems are NP-complete. We also prove W[1]-hardness for other parameterizations in the case of unbounded alphabet size. Our W[1]-hardness result for Closest Substring generalizes to Consensus Patterns, a problem arising in computational biology.

Mathematics Subject Classification (2000):

03D15 68Q17 68Q25 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Michael R. Fellows
    • 1
  • Jens Gramm†
    • 2
  • Rolf Niedermeier‡
    • 3
  1. 1.Department of Computer Science and Software EngineeringUniversity of NewcastleCallaghan 2308Australia
  2. 2.Wilhelm-Schickard-Institut für InformatikUniversität TübingenTübingenGermany
  3. 3.Institut für InformatikUniversität JenaJenaGermany

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