Article

Optimal sequencing by hybridization in rounds

Authors:

Alan M. Frieze,

Bjarni V. HalldórssonAuthors Info & Claims

RECOMB '01: Proceedings of the fifth annual international conference on Computational biology

Pages 141 - 148

https://doi.org/10.1145/369133.369187

Published: 22 April 2001 Publication History

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Abstract

Sequencing by hybridization (SBH) is a method for reconstructing a sequence over a small finite alphabet from a collection of probes (substrings). Substring queries can be arranged on an array (SBH chip) and then a combinatorial method is used to construct the sequence from its collection of probes. Technological constraints limit the number of substring queries that can be placed on a single SBH chip. We develop an idea of Margaritis and Skiena and propose an algorithm that uses a series of small SBH chips to sequence long strings while the number of probes used matches the information theoretical lower bound up to a constant factor.

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Cited By

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Skiena SSnir S(2019)Restricting SBH ambiguity via restriction enzymesDiscrete Applied Mathematics10.1016/j.dam.2005.02.034155:6-7(857-867)Online publication date: 1-Jan-2019
https://dl.acm.org/doi/10.1016/j.dam.2005.02.034
Halperin EHalperin SHartman TShamir R(2002)Handling long targets and errors in sequencing by hybridizationProceedings of the sixth annual international conference on Computational biology10.1145/565196.565219(176-185)Online publication date: 18-Apr-2002
https://dl.acm.org/doi/10.1145/565196.565219
Mignosi FRestivo ASciortino M(2002)Forbidden Factors and Fragment AssemblyRAIRO - Theoretical Informatics and Applications10.1051/ita:200113235:6(565-577)Online publication date: 15-Jul-2002
https://doi.org/10.1051/ita:2001132
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Optimal sequencing by hybridization in rounds

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Published In

RECOMB '01: Proceedings of the fifth annual international conference on Computational biology

April 2001

316 pages

ISBN:1581133537

DOI:10.1145/369133

Chairman:
Thomas Lengauer
German National Research Center for Information Technology, Germany

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 22 April 2001

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RECOMB01

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SIGACT

RECOMB01: The Fifth Annual International Conference on Computational Molecular Biology

April 22 - 25, 2001

Quebec, Montreal, Canada

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RECOMB '01 Paper Acceptance Rate 35 of 128 submissions, 27%;

Overall Acceptance Rate 148 of 538 submissions, 28%

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Cited By

View all

Skiena SSnir S(2019)Restricting SBH ambiguity via restriction enzymesDiscrete Applied Mathematics10.1016/j.dam.2005.02.034155:6-7(857-867)Online publication date: 1-Jan-2019
https://dl.acm.org/doi/10.1016/j.dam.2005.02.034
Halperin EHalperin SHartman TShamir R(2002)Handling long targets and errors in sequencing by hybridizationProceedings of the sixth annual international conference on Computational biology10.1145/565196.565219(176-185)Online publication date: 18-Apr-2002
https://dl.acm.org/doi/10.1145/565196.565219
Mignosi FRestivo ASciortino M(2002)Forbidden Factors and Fragment AssemblyRAIRO - Theoretical Informatics and Applications10.1051/ita:200113235:6(565-577)Online publication date: 15-Jul-2002
https://doi.org/10.1051/ita:2001132
Skiena SSnir S(2002)Restricting SBH Ambiguity via Restriction EnzymesAlgorithms in Bioinformatics10.1007/3-540-45784-4_30(404-417)Online publication date: 10-Oct-2002
https://doi.org/10.1007/3-540-45784-4_30

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