| Improving the design of genechip arrays by combining placement and embedding. | |
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MedLine Citation:
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PMID: 17951844 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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The microarray layout problem is a generalization of the border length minimization problem and asks to distribute oligonucleotide probes on a microarray and to determine their embeddings in the deposition sequence in such a way that the overall quality of the resulting synthesized probes is maximized. Because of its inherent computational complexity, it is traditionally attacked in several phases: partitioning, placement, and re-embedding. We present the first algorithm, Greedy+, that combines placement and embedding and results in improved layouts in terms of border length and conflict index (a more realistic measure of probe quality), both on arrays of random probes and on existing Affymetrix GeneChip arrays. We also present a large-scale study on how the layouts of GeneChip arrays have improved over time, and show how Greedy+ can further improve layout quality by as much as 8% in terms of border length and 34% in terms of conflict index. |
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Authors:
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Ségio A de Carvalho; Sven Rahmann |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference Volume: 6 ISSN: 1752-7791 ISO Abbreviation: Comput Syst Bioinformatics Conf Publication Date: 2007 |
Date Detail:
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Created Date: 2007-10-22 Completed Date: 2007-12-14 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 101294517 Medline TA: Comput Syst Bioinformatics Conf Country: United States |
Other Details:
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Languages: eng Pagination: 417-27 Citation Subset: IM |
Affiliation:
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Computational Methods for Emerging Technologies, Genome Informatics, Technische Fakultät, Bielefeld University, D-33594 Bielefeld, Germany. Sergio.Carvalho@cebitec.uni-bielefeld.de |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Base Sequence Computer-Aided Design DNA Probes / genetics* Equipment Design Equipment Failure Analysis Molecular Sequence Data Oligonucleotide Array Sequence Analysis / instrumentation*, methods* Reproducibility of Results Sensitivity and Specificity Sequence Analysis, DNA / methods* |
| Chemical | |
Reg. No./Substance:
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0/DNA Probes |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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