On the complexity of positional sequencing by hybridization

Amir Ben-Dor, Itsik Pe’er, Ron Shamir, Roded Sharan

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


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.

Original languageEnglish
Title of host publicationCombinatorial Pattern Matching - 10th Annual Symposium, CPM 1999, Proceedings
EditorsMike Paterson, Maxime Crochemore
PublisherSpringer Verlag
Number of pages13
ISBN (Print)3540662782, 9783540662785
StatePublished - 1999
Event10th Annual Symposium on Combinatorial Pattern Matching, CPM 1999 - Warwick, United Kingdom
Duration: 22 Jul 199924 Jul 1999

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference10th Annual Symposium on Combinatorial Pattern Matching, CPM 1999
Country/TerritoryUnited Kingdom


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