On the complexity of positional sequencing by hybridization

A. Ben-Dor, I. Pe’er, R. Shamir, R. Sharan

Research output: Contribution to journalArticlepeer-review

Abstract

In sequencing by hybridization (SBH), one has to reconstruct a sequence from its l-long substrings. SBH was proposed as an alternative to gel-based DNA sequencing approaches, but in its original form the method is not competitive. Positional SBH (PSBH) is a recently proposed enhancement of SBH in which one has additional information about the possible positions of each substring along the target sequence. We give a linear time algorithm for solving PSBH when each substring has at most two possible positions. On the other hand, we prove that the problem is NP-complete if each substring has at most three possible positions. We also show that PSBH is NP-complete if the set of allowed positions for each substring is an interval of length k and provide a fast algorithm for the latter problem when k is bounded.

Original languageEnglish
Pages (from-to)361-371
Number of pages11
JournalJournal of Computational Biology
Volume8
Issue number4
DOIs
StatePublished - 1 Sep 2001

Keywords

  • Complexity
  • Eulerian graphs
  • NP-hardness
  • Parameterized algorithms
  • Positional sequencing by hybridization

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