Abstract Computations and Applications of Minimal Absent Words

Abstract Computations and Applications of Minimal Absent Words

Abstract
Computations and Applications of Minimal
Absent Words
Carl Barton1 , Alice Heliou2,3 *,Laurent Mouchard4 , Solon P. Pissis
5
1
The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University
of London, UK
2
Laboratoire d’Informatique de l’École Polytechnique (LIX), CNRS UMR 7161, France
3
Inria Saclay-Île de France, AMIB, Bâtiment Alan Turing, France
4
University of Rouen, LITIS EA 4108, TIBS, Rouen, France
5
Department of Informatics, King’s College London, London, UK
*Corresponding author: [email protected]
Abstract
An absent word of a word y of length n is a word that does not occur in y. It is a
minimal absent word if all its proper factors occur in y. Minimal absent words have
been computed in genomes of organisms from all domains of life; their computation
also provides a fast alternative for measuring approximation in sequence comparison.
There exists an O(n)-time and O(n)-space algorithm for computing all minimal
absent words on a fixed-sized alphabet based on the construction of suffix array [1].
Then two other algorithms were designed: one that can be executed in parallel [2],
whose implementation achieves near-optimal speed-ups. An other that can run with
as little as 1 GB of RAM (Heliou et al. writing in process). Thus, minimal absent
words can be computed for the whole human genome on a desktop computer in a
few hours.
Here, we will briefly present these algorithms and explain the different applications
of minimal absent words.
References
[1]
C. Barton, A. Heliou, L. Mouchard, and S. P. Pissis. Linear-time computation of
minimal absent words using suffix array. BMC Bioinformatics, 15:388, 2014.
[2]
C. Barton, A. Heliou, L. Mouchard, and S. P. Pissis. Parallelising the computation
of minimal absent words. In 11th International Conference on Parallel Processing
and Applied Mathematics (PPAM 2015), 2015.
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