Optimal probing patterns for sequencing by hybridization

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3 Scopus citations

Abstract

Sequencing by Hybridization (SBH) is a method for reconstructing a DNA sequence based on its k-mer content. This content, called the spectrum of the sequence, can be obtained from hybridization with a universal DNA chip. The main shortcoming of SBH is that it reliably reconstructs only sequences of length at most square root of the size of the chip. Frieze et al. [9] showed that by using gapped probes, SBH can reconstruct sequences with length that is linear in the size of the chip. In this work we investigate the optimal placement of the gaps in the probes, and give an algorithm for finding nearly optimal gap placement. Using our algorithm, we obtain a chip design which is more efficient than the chip of Frieze et al.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings
PublisherSpringer Verlag
Pages366-375
Number of pages10
ISBN (Print)3540395830, 9783540395836
DOIs
StatePublished - 1 Jan 2006
Event6th International Workshop on Algorithms in Bioinformatics, WABI 2006 - Zurich, Switzerland
Duration: 11 Sep 200613 Sep 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4175 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference6th International Workshop on Algorithms in Bioinformatics, WABI 2006
Country/TerritorySwitzerland
CityZurich
Period11/09/0613/09/06

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