Bioinformatics Advance Access originally published online on June 20, 2006
Bioinformatics 2006 22(16):1963-1970; doi:10.1093/bioinformatics/btl289
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Transcript mapping with high-density oligonucleotide tiling arrays
1 European Molecular Biology Laboratory, European Bioinformatics Institute Cambridge CB10 1SD, UK
2 European Molecular Biology Laboratory Meyerhofstrasse 1, 69117 Heidelberg, Germany
*To whom correspondence should be addressed.
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Abstract |
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Motivation: High-density DNA tiling microarrays are a powerful tool for the characterization of complete transcriptomes. The two major analytical challenges are the segmentation of the hybridization signal along genomic coordinates to accurately determine transcript boundaries and the adjustment of the sequence-dependent response of the oligonucleotide probes to achieve quantitative comparability of the signal between different probes.
Results: We describe a dynamic programming algorithm for finding a globally optimal fit of a piecewise constant expression profile along genomic coordinates. We developed a probe-specific background correction and scaling method that employs empirical probe response parameters determined from reference hybridizations with no need for paired mismatch probes. This combined analysis approach allows the accurate determination of dynamical changes in transcription architectures from hybridization data and will help to study the biological significance of complex transcriptional phenomena in eukaryotic genomes.
Availability: R package tilingArray at http://www.bioconductor.org.
Contact: huber{at}ebi.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Associate Editor: Joaquin Dopazo
Received on April 3, 2006; accepted on June 20, 2006
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