Bounds for resequencing by hybridization

Dekel Tsur

doi:10.1007/978-3-540-39763-2_35

Bounds for resequencing by hybridization

Dekel Tsur

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

We study the problem of finding the sequence of an unknown DNA fragment given the set of its k-long subsequences and a homologous sequence, namely a sequence that is similar to the target sequence. Such a sequence is available in some applications, e.g., when detecting single nucleotide polymorphisms. Pe'er and Shamir studied this problem and presented a heuristic algorithm for it. In this paper, we give an algorithm with provable performance: We show that under some assumptions, the algorithm can reconstruct a random sequence of length O(4^k) with high probability. We also show that no algorithm can reconstruct sequences of length Ω(log k· 4^k).

Original language	English
Pages (from-to)	498-511
Number of pages	14
Journal	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	2812
DOIs	https://doi.org/10.1007/978-3-540-39763-2_35
State	Published - 1 Jan 2003
Externally published	Yes

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

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10.1007/978-3-540-39763-2_35

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Bounds for resequencing by hybridization

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