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Evolving regular expressions for genechip probe performance prediction

Langdon, WB and Harrison, AP (2008) Evolving regular expressions for genechip probe performance prediction. In: UNSPECIFIED, ? - ?.

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Abstract

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 concordance indicates a poor probe. Regular expressions can be data mined by a Backus-Naur form (BNF) context-free grammar using strongly typed genetic programming written in gawk and using egrep. 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. © 2008 Springer-Verlag Berlin Heidelberg.

Item Type: Conference or Workshop Item (UNSPECIFIED)
Additional Information: Published proceedings: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Subjects: Q Science > QA Mathematics
Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science and Health > Mathematical Sciences, Department of
Depositing User: Jim Jamieson
Date Deposited: 04 Oct 2011 15:14
Last Modified: 06 Feb 2019 00:15
URI: http://repository.essex.ac.uk/id/eprint/835

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