Langdon, WB and Harrison, AP (2009) Evolving DNA motifs to predict GeneChip probe performance. Algorithms for Molecular Biology, 4 (1). 6-. DOI https://doi.org/10.1186/1748-7188-4-6
Langdon, WB and Harrison, AP (2009) Evolving DNA motifs to predict GeneChip probe performance. Algorithms for Molecular Biology, 4 (1). 6-. DOI https://doi.org/10.1186/1748-7188-4-6
Langdon, WB and Harrison, AP (2009) Evolving DNA motifs to predict GeneChip probe performance. Algorithms for Molecular Biology, 4 (1). 6-. DOI https://doi.org/10.1186/1748-7188-4-6
Abstract
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 Faculty of Science and Health > Mathematics, Statistics and Actuarial Science, School of |
| SWORD Depositor: | Unnamed user with email elements@essex.ac.uk |
| Depositing User: | Unnamed user with email elements@essex.ac.uk |
| Date Deposited: | 29 Sep 2011 15:37 |
| Last Modified: | 04 Dec 2024 06:18 |
| URI: | http://repository.essex.ac.uk/id/eprint/829 |
Available files
Filename: PMC2679018.pdf
Licence: Creative Commons: Attribution 3.0