Missing pattern discovery

Authors:
Stanislav Angelov;Shunsuke Inenaga;Teemu Kivioja;Veli Mäkinen
Affiliations:
Department of Computer and Information Science, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA;Graduate School of Information Science and Electrical Engineering, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan;Genome-Scale Biology Program, Biomedicum Helsinki, P.O. Box 63 (Haartmaninkatu 8), FIN-00014 University of Helsinki, Finland and Department of Computer Science, P.O. Box 68 (Gustaf Hällstr ...;Department of Computer Science, P.O. Box 68 (Gustaf Hällströmin katu 2b), FIN-00014 University of Helsinki, Finland
Venue:
Journal of Discrete Algorithms
Year:
2011

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Abstract

In this paper, we study the missing patterns problem: Find the shortest pair of patterns that do not occur close to each other in a given text, i.e., the distance between their occurrences is always greater than a given threshold @a. We present various solutions to this problem, as well as to the case where the patterns in the pair are required to be of the same length. This work is motivated by optimizing the sensitivity of PCR. Experiments show that our algorithm is practical enough to handle human genome data.