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Repeatfinding

Part 4. Bioinformatics

4.1. Genome Assembly and Sequencing

Basic Techniques and Approaches

  1. Richard Sucgang

Published Online: 15 JUL 2005

DOI: 10.1002/047001153X.g401402

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Sucgang, R. 2005. Repeatfinding. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.1:9.

Author Information

  1. Baylor College of Medicine, Houston, TX, USA

Publication History

  1. Published Online: 15 JUL 2005

Abstract

Finding repeats in biological sequences is a necessary first step in recognizing patterns and biologically relevant motifs. Given the inexact nature of biological repeats, the software required to detect, identify, classify, and curate them have grown not only in variety but in sophistication as well, accommodating increases both in amount of data and available computing power. Open source and free-for-academic-use programs implementing repeat finding algorithms, as well as databases that curate known biological repeat motifs are surveyed in this section.

Keywords:

  • EMBOSS package;
  • REPuter package;
  • MUMmer package;
  • RepeatMasker;
  • RepeatFinder