Repseek, A tool to retrieve approximate repeats from large DNA sequences. 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 all approximate repeats in DNA sequences allowing for gaps and a substitution matrix and using a statistical framework. Here, we present an implementation of a two-steps method (seed detection followed by their extensions) 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.
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References in zbMATH (referenced in 3 articles )
Showing results 1 to 3 of 3.
- Federico, Maria; Peterlongo, Pierre; Pisanti, Nadia; Sagot, Marie-France: Rime: repeat identification (2014)
- Achaz, Guillaume; Boyer, Frédéric; Rocha, Eduardo P.C.; Viari, Alain; Coissac, Eric: Repseek, a tool to retrieve approximate repeats from large DNA sequences (2007)
- Spouge, John L.: Markov additive processes and repeats in sequences (2007)