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.
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This work was supported by the Korea Research Foundation Grant funded by the Korean Government(MOEHRD)(KRF-2005-041-D00747).
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References
Debouck, C., Goodfellow, P.N.: DNA microarrays in drug discovery and development. Nature Genetics 21, 48–50 (1999)
Gasieniec, L., Li, C.Y., Sant, P., Wong, P.W.H.: Efficient Probe Selection in Microarray Design. In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, IEEE Computer Society Press, Los Alamitos (2006)
Hamming, R.W.: Error-detecting and error-correcting codes. Bell System Technical Journal 29(2), 147–160 (1950)
Kaderali, L., Schliep, A.: Selecting signature oligonucleotides to identify organisms using DNA arrays. Bioinformatics 18(10), 1340–1349 (2002)
Li, L., Stormo, G.: Selection of optimal DNA oligos for gene expression analysis. Bioinformatics 17(11), 1067–1076 (2001)
Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H., Brown, E.L.: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology 14, 1675–1680 (1996)
Manber, U., Myers, G.: Suffix arrays: a new method for online string serarches. SIAM Journal of Computing 22(5), 935–948 (1993)
Mount, D.W.: Bioinformatics Sequence and Genome Analysis, 2nd edn. CSHLPress (2004)
Rahmann, S.: Rapid large-scale oligonucleotide selection for microarrays. In: Proc. IEEE Computer Society Bioinformatics Conference, vol. 1, pp. 54–63. IEEE Computer Society Press, Los Alamitos (2002)
Rahmann, S.: Fast and sensitive probe selection for DNA chips using jumps in matching statistics. In: Proc. IEEE Computational Systems Bioinformatics, vol. 2, pp. 57–64. IEEE Computer Society Press, Los Alamitos (2003)
SantaLucia, J.J., Allawi, H.T., Seneviratne, P.A.: Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability. Biochemistry 35, 3555–3562 (1996)
Stekel, D.: Microarray Bioinformatics. Cambridge (2003)
Sung, W., Lee, W.: Fast and accurate probe selection algorithm for large genomes. Proc. IEEE Computational Systems Bioinformatics 2, 65–74 (2003)
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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
Publisher Name: Springer, Berlin, Heidelberg
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