TY - CHAP

T1 - Finding missing patterns

AU - Inenaga, Shunsuke

AU - Kivioja, Teemu

AU - Mäkinen, Veli

PY - 2004

Y1 - 2004

N2 - Consider the following problem: Find the shortest pattern that does not occur in a given text. To make the problem non-trivial, the pattern is required to consist only of characters that occur in the text. This problem can be solved easily in linear time using the suffix tree of the text. In this paper, we study an extension of this problem, namely 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 show that the missing patterns problem can be solved in O(min(αn log n, n2)) time, where n is the size of the text. For the special case where both pairs are required to have the same length, we give an algorithm with time complexity O(αn log log n). The problem is motivated by optimization of multiplexed nested-PCR.

AB - Consider the following problem: Find the shortest pattern that does not occur in a given text. To make the problem non-trivial, the pattern is required to consist only of characters that occur in the text. This problem can be solved easily in linear time using the suffix tree of the text. In this paper, we study an extension of this problem, namely 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 show that the missing patterns problem can be solved in O(min(αn log n, n2)) time, where n is the size of the text. For the special case where both pairs are required to have the same length, we give an algorithm with time complexity O(αn log log n). The problem is motivated by optimization of multiplexed nested-PCR.

UR - http://www.scopus.com/inward/record.url?scp=33646730028&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33646730028&partnerID=8YFLogxK

U2 - 10.1007/978-3-540-30219-3_39

DO - 10.1007/978-3-540-30219-3_39

M3 - Chapter

AN - SCOPUS:33646730028

SN - 3540230181

SN - 9783540230182

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 463

EP - 474

BT - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

A2 - Jonassen, Inge

A2 - Kim, Junhyong

PB - Springer Verlag

ER -