Reference Work Entry

Encyclopedia of Algorithms

pp 1-99

Approximate Tandem Repeats

2001; Landau, Schmidt, Sokol 2003; Kolpakov, Kucherov
  • Gregory KucherovAffiliated withLIFL and INRIA
  • , Dina SokolAffiliated withDepartment of Computer and Information Science, Brooklyn College of CUNY

Keywords and Synonyms

Approximate repetitions; Approximate periodicities   

Problem Definition

Identification of periodic structures in words (variants of which are known as tandem repeats, repetitions, powers or runs) is a fundamental algorithmic task (see entry Squares and Repetitions). In many practical applications, such as DNA sequence analysis, considered repetitions admit a certain variation between copies of the repeated pattern. In other words, repetitions under interest are approximate tandem repeats and not necessarily exact repeats only.

The simplest instance of an approximate tandem repeat is an approximate square. An approximate square in a word w is a subword uv, where u and v are within a given distance k according to some distance measure between words, such as Hamming distance or edit (also called Levenstein) distance. There are several ways to define approximate tandem repeats as successions of approximate squ ...

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