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© Research
Publication : Bioinformatics (Oxford, England)

Repseek, a tool to retrieve approximate repeats from large DNA sequences

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Bioinformatics (Oxford, England) - 11 Oct 2006

Achaz G, Boyer F, Rocha EP, Viari A, Coissac E

Link to Pubmed [PMID] – 17038345

Bioinformatics 2007 Jan;23(1):119-21

Chromosomes or other long DNA sequences contain many highly similar repeated sub-sequences. While there are efficient methods for detecting strict repeats or detecting already characterized repeats, there is no software available for detecting approximate repeats in large DNA sequences allowing for weighted substitutions and indels in a coherent statistical framework. Here, we present an implementation of a two-steps method (seed detection followed by their extension) that detects those approximate repeats. Our method is computationally efficient enough to handle large sequences and is flexible enough to account for influencing factors, such as sequence-composition biases both at the seed detection and alignment levels.

http://www.ncbi.nlm.nih.gov/pubmed/17038345