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Lossless filter for multiple repeats with bounded edit distance |
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| Authors: | Pierre Peterlongo Gustavo Akio Tominaga Sacomoto Alair Pereira do Lago Nadia Pisanti Marie-France Sagot |
| Affiliation: | 1. équipe-projet Symbiose, IRISA/CNRS, Campus de Beaulieu, Rennes, France 2. Curso Experimental de Ciências Moleculares da Universidade de S?o, Paulo, Brazil 3. Instituto de Matemática e Estatística da Universidade de S?o, Paulo, Brazil 4. Dipartimento di Informatica, Università di, Pisa, Italy 5. équipe BAOBAB, Laboratoire de Biométrie et Biologie Evolutive (UMR 5558);, CNRS; Univ. Lyon 1, Villeurbanne Cedex, France 6. équipe-Projet BAMBOO, INRIA, Rh?ne-Alpes, France |
| Abstract: | BackgroundIdentifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and of their phylogenetic relationship. Finding such fragments while allowing for a certain number of insertions, deletions, and substitutions, is however known to be a computationally expensive task, and consequently exact methods can usually not be applied in practice. |
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