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An Algorithm for Spot Addressing in Microarray using Regular Grid Structure Searching  

진희정 (부산대학교 전자계산학과)
조환규 (부산대학교 전기전자정보컴퓨터공학부)
Publication Information
Journal of KIISE:Computer Systems and Theory / v.31, no.9, 2004 , pp. 514-526 More about this Journal
Abstract
Microarray is a new technique for gene expression experiment, which has gained biologist's attention for recent years. This technology enables us to obtain hundreds and thousands of expression of gene or genotype at once using microarray Since it requires manual work to analyze patterns of gene expression, we want to develop an effective and automated tools to analyze microarray image. However it is difficult to analyze DNA chip images automatically due to several problems such as the variation of spot position, the irregularity of spot shape and size, and sample contamination. Especially, one of the most difficult problems in microarray analysis is the block and spot addressing, which is performed by manual or semi automated work in all the commercial tools. In this paper we propose a new algorithm to address the position of spot and block using a new concept of regular structure grid searching. In our algorithm, first we construct maximal I-regular sequences from the set of input points. Secondly we calculate the rotational angle and unit distance. Finally, we construct I-regularity graph by allowing pseudo points and then we compute the spot/block address using this graph. Experiment results showed that our algorithm is highly robust and reliable. Supplement information is available on http://jade.cs.pusan.ac.kr/~autogrid.
Keywords
bioinformatics; Image processing; DNA microarray; regular grid structure;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
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