Optimal sequencing by hybridization in rounds

Alan M. Frieze, Bjarni V. Halldórsson*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)355-369
Number of pages15
JournalJournal of Computational Biology
Issue number2
Publication statusPublished - 2002

Other keywords

  • DNA sequencing
  • Probabilistic analysis
  • Sequencing by hybridization


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