Faster algorithms for computing maximal multirepeats in multiple sequences
MetadataShow full item record
A repeat in a string is a substring that occurs more than once. A repeat is extendible if every occurrence of the repeat has an identical letter either on the left or on the right; otherwise, it is maximal. A multirepeat is a repeat that occurs at least mmin times (mmin greater than/equal to 2) in each of at least q greater than/equal to 1 strings in a given set of strings. In this paper, we describe a family of efficient algorithms based on suffix arrays to compute maximal multirepeats under various constraints. Our algorithms are faster, more flexible and much more space-efficient than algorithms recently proposed for this problem. The results extend recent work by two of the authors computing all maximal repeats in a single string.
Showing items related by title, author, creator and subject.
Puglisi, Simon; Smyth, William; Yusufu, M. (2010)Given a string x = x[1..n] on an alphabet of size α, and a threshold p min ≥ 1, we describe four variants of an algorithm PSY1 that, using a suffix array, computes all the complete nonextendible repeats in x of length p ...
Crochemore, M.; Iliopoulos, Costas; Pissis, S.; Tischler, G. (2010)A proper fact or u of a string y is a cover of y if every letter of y is within some occurrence of u in y. The concept generalises the notion of periods of a string. An integer array C is the minimal-cover (resp. ...
Puglisi, Simon; Smyth, Bill; Yusufu, M. (2008)Given a string x = x[1..n] on an alphabet of size a, and a threshold pmin = 1, we first describe a new algorithm PSY1 that, based on suffix array construction, computes all the complete nonextendible repeats in x of length ...