A first approach to finding common motifs with gaps

Document Type

Article

Publication Date

12-1-2005

Abstract

We present three linear algorithms for as many formulations of the problem of finding motifs with gaps. The three versions of the problem are distinct in that they assume different constraints on the size of the gaps. The outline of the algorithm is always the same, although this is adapted each time to the specific problem, while maintaining a linear time complexity with respect to the input size. The approach we suggest is based on a re-writing of the text that uses a new alphabet made of labels representing words of the original input text. The computational complexity of the algorithm allows the use of it also to find long motifs. The algorithm is in fact general enough that it could be applied to several variants of the problem other than those suggested in this paper. © World Scientific Publishing Company.

Identifier

33746189871 (Scopus)

Publication Title

International Journal of Foundations of Computer Science

External Full Text Location

https://doi.org/10.1142/S0129054105003716

ISSN

01290541

First Page

1145

Last Page

1154

Issue

6

Volume

16

Grant

PST.CLG.977017

Fund Ref

North Atlantic Treaty Organization

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