title: Optimal sequencing by hybridization in rounds.
abstract: Sequencing by hybridization (SBH) is a method for sequencing DNA. The Watson-Crick complementarity of DNA can be used to determine whether the DNA contains an oligonucleotide substring. A large number of oligonucleotides can be arranged on an array (SBH chip). A combinatorial method is used to construct the sequence from the collection of probes that occur in it. We develop an idea of Margaritis and Skiena and propose an algorithm that uses a series of small SBH chips to sequence long strings. The total number of probes used by our method matches the information theoretical lower bound up to a constant factor.
authors.affiliation: Department of Mathematical Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
authors.forename: Alan M
authors.initials: AM
authors.lastname: Frieze
authors.forename: Bjarni V
authors.initials: BV
authors.lastname: Halldórsson
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D004247:DNA / Q000235:genetics; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data*
chemical_list: D004247:DNA