A fast preprocessing algorithm to select gene-specific probes of DNA microarrays

Authors:
Seung-Ho Kang;In-Seon Jeong;Mun-Ho Choi;Hyeong-Seok Lim
Affiliations:
Dept. of Computer Science, Chonnam National University, Gwangju, Korea;Dept. of Computer Science, Chonnam National University, Gwangju, Korea;Dept. of Computer Science, Chonnam National University, Gwangju, Korea;Dept. of Computer Science, Chonnam National University, Gwangju, Korea
Venue:
FAW'07 Proceedings of the 1st annual international conference on Frontiers in algorithmics
Year:
2007

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Abstract

The performance of a DNA microarray is dependent on the quality of the probes it uses. A good probe is uniquely associated with a particular sequence that distinguishes it from other sequences. Most existing algorithms to solve the probe selection problem use the common approach that directly filters out "bad" probes or selects "good" probes of each gene. However, this approach requires a very long running time for large genomes. We propose a novel approach that screens out a "bad" gene(not probe) set for each gene before filtering out bad probes. We also provide a O(1/4qN2)time preprocessing algorithm for this purpose using q-gram for a length-N genome, guaranteeing more than 95% sensitivity. The screened bad gene sets can be used as inputs to other probe selection algorithms in order to select the specific probes of each gene.