Irredundant tandem motifs

Eliminating the possible redundancy from a set of candidate motifs occurring in an input string is fundamental in many applications. The existing techniques proposed to extract irredundant motifs are not suitable when the motifs to search for are structured, i.e., they are made of two (or several) s...

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Veröffentlicht in:Theoretical computer science Jg. 525; S. 89 - 102
Hauptverfasser: Parida, Laxmi, Pizzi, Cinzia, Rombo, Simona E.
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Elsevier B.V 13.03.2014
Schlagworte:
Irredundant
Motifs
Patterns
Redundant motifs
String algorithm
Suffix tree
Tandem
Redundant motifs
String algorithm
Suffix tree
Motifs
Tandem
Irredundant
Patterns
ISSN:0304-3975, 1879-2294
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Beschreibung
Zusammenfassung:Eliminating the possible redundancy from a set of candidate motifs occurring in an input string is fundamental in many applications. The existing techniques proposed to extract irredundant motifs are not suitable when the motifs to search for are structured, i.e., they are made of two (or several) subwords that co-occur in a text string s of length n. The main effort of this work is studying and characterizing a compact class of tandem motifs, that is, pairs of substrings 〈m1,m2〉 occurring in tandem within a maximum distance of d symbols in s, where d is an integer constant given in input. To this aim, we first introduce the concept of maximality, related to four specific conditions that hold only for this class of motifs. Then, we eliminate the remaining redundancy by defining the notion of irredundancy for tandem motifs. We prove that the number of non-overlapping irredundant tandem motifs is O(d2n) which, considering d as a constant, leads to a linear number of tandems in the length of the input string. This is an order of magnitude less than previously developed compact indexes for tandem extraction. The notions and bounds provided for tandem motifs are generalized for the case r⩾2, if r is the number of subwords composing the motifs. Finally, we also provide an algorithm to extract irredundant tandem motifs.
ISSN:0304-3975
1879-2294
DOI:10.1016/j.tcs.2013.08.012