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Evolving DNA motifs to predict GeneChip probe performance

Langdon, WB and Harrison, AP (2009) 'Evolving DNA motifs to predict GeneChip probe performance.' Algorithms for Molecular Biology, 4. ISSN 1748-7188

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Background: Affymetrix High Density Oligonuclotide Arrays (HDONA) simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 human tissue samples from NCBI's GEO database to indicated the quality of individual HG-U133A probes. Low correlation indicates a poor probe. Results: Regular expressions can be automatically created from a Backus-Naur form (BNF) context-free grammar using strongly typed genetic programming. Conclusion: The automatically produced motif is better at predicting poor DNA sequences than an existing human generated RE, suggesting runs of Cytosine and Guanine and mixtures should all be avoided. © 2009 Langdon and Harrison; licensee BioMed Central Ltd.

Item Type: Article
Subjects: Q Science > QA Mathematics
Q Science > QH Natural history > QH301 Biology
Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science and Health > Mathematical Sciences, Department of
Depositing User: Jim Jamieson
Date Deposited: 29 Sep 2011 15:37
Last Modified: 23 Jan 2019 00:17

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