Lossless filter for multiple repetitions with Hamming distance

Pierre Peterlongo (1) , Nadia Pisanti (2) , Frédéric Boyer (3) , Alair Pereira Do Lago (4) , Marie-France Sagot (3)

1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
2 Department of Computer Science [Pisa]
3 HELIX - Computer science and genomics
4 IME/USP - Departamento de Ciência da Computação [São Paulo]

Similarity search in texts, notably in biological sequences, has received substantial attention in the last few years. Numerous filtration and indexing techniques have been created in order to speed up the solution of the problem. However, previous filters were made for speeding up pattern matching, or for finding repetitions between two strings or o ccurring twice in the same string. In this paper, we present an algorithm called Nimbus for filtering strings prior to finding repetitions o ccurring twice or more in a string, or in two or more strings. Nimbus uses gapped seeds that are indexed with a new data structure, called a bi-factor array, that is also presented in this paper. Experimental results show that the filter can be very efficient: preprocessing with Nimbus a data set where one wants to find functional elements using a multiple lo cal alignment to ol such as Glam, the overall execution time can be reduced from 7.5 hours to 2 minutes.

Mots clés: Approximate repetitions; k-Factors; Multiple local alignment; Bi-factors; Bi-factor array

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Pierre Peterlongo, Nadia Pisanti, Frédéric Boyer, Alair Pereira Do Lago, Marie-France Sagot. Lossless filter for multiple repetitions with Hamming distance. Journal of Discrete Algorithms, 2008, 6 (3), pp.497-509. ⟨10.1016/j.jda.2007.03.003⟩. ⟨inria-00179731⟩