Classification method for microarray probe selection using sequence, thermodynamics and secondary structure parameters

Gupta, L., Kumar, S., Singh, R., Shaik, R., Dimitrova, N., Gorthi, A., Lakshmi, B., Pai, D., Kamalakaran, S., Zhao, X., Wigler, M. H. (December 2008) Classification method for microarray probe selection using sequence, thermodynamics and secondary structure parameters. 19th International Conference on Pattern Recognition. ISSN 1051-4651

URL: http://ieeexplore.ieee.org/document/4761758/
DOI: 10.1109/ICPR.2008.4761758

Abstract

Probe design is the most important step for any microarray based assay. Accurate and efficient probe design and selection for the target sequence is critical in generating reliable and useful results. Several different approaches for probe design are reported in literature and an increasing number of bioinformatics tools are available for the same. However, based on the reported low accuracy, determining the hybridization efficiency of the probes is still a big computational challenge. Present study deals with the extraction of various novel features related to sequence composition, thermodynamics and secondary structure that may be essential for designing good probes. A feature selection method has been used to assess the relative importance of all these features. In this paper, we validate the importance of various features currently used for designing an oligonucleotide probe. Finally, a classification methodology is presented that can be used to predict the hybridization quality of a probe.

Item Type: Paper
Subjects: Investigative techniques and equipment
bioinformatics > genomics and proteomics > analysis and processing > microarray gene expression processing
Investigative techniques and equipment > probes > DNA probes
Publication Type > Meeting Abstract
CSHL Authors:
Communities: CSHL labs > Wigler lab
Depositing User: CSHL Librarian
Date: December 2008
Date Deposited: 12 Apr 2012 18:52
Last Modified: 16 Mar 2018 16:11
URI: http://repository.cshl.edu/id/eprint/26190

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