On the complexity of positional sequencing by hybridization.
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.
Ben-Dor
A
A
Agilent Laboratories.
Pe'er
I
I
Shamir
R
R
Sharan
R
R
D000465:Algorithms; D019295:Computational Biology; D009693:Nucleic Acid Hybridization; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000706:statistics & numerical data