TAILIEUCHUNG - Báo cáo sinh học: " Evolving DNA motifs to predict GeneChip probe performance"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: Evolving DNA motifs to predict GeneChip probe performance. | Algorithms for Molecular Biology BioMed Central Research Evolving DNA motifs to predict GeneChip probe performance WB Langdon 1 and AP Harrison2 Address Department of Computer Science King s College London Strand London WC2R 2LS UK and 2Biological Sciences University of Essex Wivenhoe Park Colchester CO4 3SQ UK Email WB Langdon - wlangdon@ AP Harrison - harry@ Corresponding author Open Access Published 19 March 2009 Received 20 November 2008 Algorithms for Molecular Biology 2009 4 6 doi l748-7l 88-4-6 Accepted 19 March 2009 This article is available from http content 4 l 6 2009 Langdon and Harrison licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. 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. Background Typically Affymetrix GeneChips . HG-U133A measure gene expression at least eleven points along the gene. Individual measurements are given by short 25 base DNA sequences known as probes. These are complementary to corresponding locations in .

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