Title :
Finding repeats with fixed gap
Author :
Kolpakov, Roman ; Kucherov, Gregory
Author_Institution :
Inst. for Inf. & Appl. Math., Moscow Univ., Russia
Abstract :
We propose an algorithm for finding, within a word, all pairs of occurrences of the same subword within a given distance r. The obtained complexity is O(n log r + S), where S is the size of the output. We also show how the algorithm can be modified in order to find all such pairs of occurrences separated by a given word. The solution uses an algorithm for finding all quasi-squares in two strings, a problem that generalizes the well-known problem of searching for squares
Keywords :
computational complexity; search problems; string matching; complexity; fixed gap; occurrence pairs; output size; quasi-squares; searching; strings; subword occurrence repeats; Binary search trees; Biology computing; Combinatorial mathematics; Informatics; Sequences;
Conference_Titel :
String Processing and Information Retrieval, 2000. SPIRE 2000. Proceedings. Seventh International Symposium on
Conference_Location :
A Curuna
Print_ISBN :
0-7695-0746-8
DOI :
10.1109/SPIRE.2000.878192
