Encyclopedia of Algorithms

Living Edition
| Editors: Ming-Yang Kao

Approximate Tandem Repeats

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DOI: https://doi.org/10.1007/978-3-642-27848-8_24-2
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Years and Authors of Summarized Original Work

  • 2001; Landau, Schmidt, Sokol

  • 2003; Kolpakov, Kucherov

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 kaccording to some distance measure between words, such as Hamming distance or edit (also called Levenshtein) distance. There are several ways to define approximate tandem repeats as successions of approximate squares, i.e., to generalize to...

Keywords

Approximate repetitions Approximate periodicities 
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Notes

Acknowledgements

This work was supported in part by the National Science Foundation Grant DB&I 0542751.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.CNRS/LIGMUniversité Paris-EstMarne-la-ValléeFrance
  2. 2.Department of Computer and Information ScienceBrooklyn College of CUNYBrooklyn ,NYUSA