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Design of a Combinatorial DNA Microarray for Protein-DNA Interaction Studies

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dc.contributor.author Mintseris, Julian en_US
dc.contributor.author Eisen, Michael B en_US
dc.date.accessioned 2012-01-11T21:09:33Z
dc.date.available 2012-01-11T21:09:33Z
dc.date.copyright 2006 en_US
dc.date.issued 2006-10-3 en_US
dc.identifier.citation Mintseris, Julian, Michael B Eisen. "Design of a combinatorial DNA microarray for protein-DNA interaction studies" BMC Bioinformatics 7:429. (2006) en_US
dc.identifier.issn 1471-2105 en_US
dc.identifier.uri http://hdl.handle.net/2144/3193
dc.description.abstract BACKGROUND. Discovery of precise specificity of transcription factors is an important step on the way to understanding the complex mechanisms of gene regulation in eukaryotes. Recently, double-stranded protein-binding microarrays were developed as a potentially scalable approach to tackle transcription factor binding site identification. RESULTS. Here we present an algorithmic approach to experimental design of a microarray that allows for testing full specificity of a transcription factor binding to all possible DNA binding sites of a given length, with optimally efficient use of the array. This design is universal, works for any factor that binds a sequence motif and is not species-specific. Furthermore, simulation results show that data produced with the designed arrays is easier to analyze and would result in more precise identification of binding sites. CONCLUSION. In this study, we present a design of a double stranded DNA microarray for protein-DNA interaction studies and show that our algorithm allows optimally efficient use of the arrays for this purpose. We believe such a design will prove useful for transcription factor binding site identification and other biological problems. en_US
dc.description.sponsorship Department of Energy Computational Science Graduate Fellowship en_US
dc.language.iso en en_US
dc.publisher BioMed Central en_US
dc.rights Copyright 2006 Mintseris and Eisen; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. en_US
dc.rights.uri http://creativecommons.org/licenses/by/2.0 en_US
dc.title Design of a Combinatorial DNA Microarray for Protein-DNA Interaction Studies en_US
dc.type article en_US
dc.identifier.doi 10.1186/1471-2105-7-429 en_US
dc.identifier.pubmedid 17018151 en_US
dc.identifier.pmcid 1635571 en_US


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Copyright 2006 Mintseris and Eisen; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Except where otherwise noted, this item's license is described as Copyright 2006 Mintseris and Eisen; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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