ArticleAlgorithms for molecular biology : AMB2009
Evolving DNA motifs to predict GeneChip probe performance.
Article in Algorithms for molecular biology : AMB, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundAffymetrix 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.
resultsRegular expressions can be automatically created from a Backus-Naur form (BNF) context-free grammar using strongly typed genetic programming.
conclusionThe 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.
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