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(1/4q N 2)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.
This work was supported by the Korea Research Foundation Grant funded by the Korean Government(MOEHRD)(KRF-2005-041-D00747).
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Kang, SH., Jeong, IS., Choi, MH., Lim, HS. (2007). A Fast Preprocessing Algorithm to Select Gene-Specific Probes of DNA Microarrays. In: Preparata, F.P., Fang, Q. (eds) Frontiers in Algorithmics. FAW 2007. Lecture Notes in Computer Science, vol 4613. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73814-5_2
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DOI: https://doi.org/10.1007/978-3-540-73814-5_2
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