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  • Title: On the complexity of positional sequencing by hybridization.
    Author: Ben-Dor A, Pe'er I, Shamir R, Sharan R.
    Journal: J Comput Biol; 2001; 8(4):361-71. PubMed ID: 11571072.
    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.
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