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  Optimal robust non-unique probe selection using Integer Linear Programming

Klau, G. W., Rahmann, S., Schliep, A., Vingron, M., & Reinert, K. (2004). Optimal robust non-unique probe selection using Integer Linear Programming. Bioinformatics, 20(Suppl.), i186-i193.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-87F9-7 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-87FA-5
Genre: Conference Paper

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 Creators:
Klau, Gunnar W., Author
Rahmann, Sven1, Author              
Schliep, Alexander1, Author              
Vingron, Martin2, Author              
Reinert, Knut, Author
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              
2Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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 Abstract: Motivation: Besides their prevalent use for analyzing gene expression, microarrays are an efficient tool for biological, medical and industrial applications due to their ability to assess the presence or absence of biological agents, the targets, in a sample. Given a collection of genetic sequences of targets one faces the challenge of finding short oligonucleotides, the probes, which allow detection of targets in a sample. Each hybridization experiment determines whether the probe binds to its corresponding sequence in the target. Depending on the problem, the experiments are conducted using either unique or non-unique probes and usually assume that only one target is present in the sample. The problem at hand is to compute a design, i.e. a minimal set of probes that allows to infer the targets in the sample from the result of the hybridization experiment. If we allow to test for more than one target in the sample, the design of the probe set becomes difficult in the case of non-unique probes. Results: Building upon previous work on group testing for microarrays, we describe the first approach to select a minimal probe set for the case of non-unique probes in the presence of a small number of multiple targets in the sample. The approach is based on an ILP formulation and a branch-and-cut algorithm. Our preliminary implementation greatly reduces the number of probes needed while preserving the decoding capabilities.

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Language(s): eng - English
 Dates: 2004-08-01
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: eDoc: 226569
DOI: 10.1093/bioinformatics/bth936
 Degree: -

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Title: Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology
Place of Event: Glasgow, UK
Start-/End Date: 2004-07-31 - 2004-08-04

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Title: Bioinformatics
Source Genre: Journal
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Pages: i186-i193 Volume / Issue: 20 (Suppl.) Sequence Number: - Start / End Page: i186 - i193 Identifier: ISSN: 1367-4803