Lossless filter for multiple repeats with bounded edit distance - Inria - Institut national de recherche en sciences et technologies du numérique Access content directly
Journal Articles Algorithms for Molecular Biology Year : 2009

Lossless filter for multiple repeats with bounded edit distance


Identifying 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.
The filter TUIUIU that we introduce in this paper provides a possible solution to this problem. It can be used as a preprocessing step to any multiple alignment or repeats inference method, eliminating a possibly large fraction of the input that is guaranteed not to contain any approximate repeat. It consists in the verification of several strong necessary conditions that can be checked in a fast way. We implemented three versions of the filter. The first is simply a straightforward extension to the case of multiple sequences of an application of conditions already existing in the literature. The second uses a stronger condition which, as our results show, enable to filter sensibly more with negligible (if any) additional time. The third version uses an additional condition and pushes the sensibility of the filter even further with a non negligible additional time in many circumstances; our experiments show that it is particularly useful with large error rates. The latter version was applied as a preprocessing of a multiple alignment tool, obtaining an overall time (filter plus alignment) on average 63 and at best 530 times smaller than before (direct alignment), with in most cases a better quality alignment.
To the best of our knowledge, TUIUIU is the first filter designed for multiple repeats and for dealing with error rates greater than 10% of the repeats length.
Fichier principal
Vignette du fichier
1748-7188-4-3.pdf (666.62 Ko) Télécharger le fichier
1748-7188-4-3.xml (287.76 Ko) Télécharger le fichier
Origin Publisher files allowed on an open archive
Format Other

Dates and versions

hal-00784457 , version 1 (04-02-2013)



Pierre Peterlongo, Gustavo Akio Tominaga Sacomoto, Alair Pereira Do Lago, Nadia Pisanti, Marie-France Sagot. Lossless filter for multiple repeats with bounded edit distance. Algorithms for Molecular Biology, 2009, 4 (1), pp.3. ⟨10.1186/1748-7188-4-3⟩. ⟨hal-00784457⟩
432 View
146 Download



Gmail Mastodon Facebook X LinkedIn More