On the Complexity of Positional Sequencing by Hybridization

Authors:
Amir Ben-Dor;Itsik Pe'er;Ron Shamir;Roded Sharan
Affiliations:
-;-;-;-
Venue:
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
Year:
1999

Citing 2
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Abstract

In sequencing by hybridization (SBH), one has to reconstruct a sequence from its k-long substrings. SBH was proposed as a promising alternative to gel-based DNA sequencing approaches, but in its original form the method is not competitive. Positional SBH 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 the positional SBH problem 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.