Efficient computation of shortest absent words in a genomic sequence

Wu, Zongda; Jiang, Tao; Su, Wujie

doi:10.1016/j.ipl.2010.05.008

Cited by 23 publications

(17 citation statements)

References 8 publications

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“…Moreover it was shown that the set of all minimal absent words of y is sufficient to uniquely reconstruct y [10,14]. The notion has been used in data compression [11,29] and in molecular biology [17,19,34,32,8,2,18], where authors often focus on the computation of the shortest absent words (sometimes called unwords).…”

Section: Introductionmentioning

confidence: 99%

Minimal Absent Words in a Sliding Window and Applications to On-Line Pattern Matching

Crochemore

Héliou

Kucherov

et al. 2017

Fundamentals of Computation Theory

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International audienceAn absent (or forbidden) word of a word y is a word that does not occur in y. It is then called minimal if all its proper factors occur in y. There exist linear-time and linear-space algorithms for computing all minimal absent words of y (Crochemore et al. in Inf Process Lett 67:111–117, 1998; Belazzougui et al. in ESA 8125:133–144, 2013; Barton et al. in BMC Bioinform 15:388, 2014). Minimal absent words are used for data compression (Crochemore et al. in Proc IEEE 88:1756–1768, 2000, Ota and Morita in Theoret Comput Sci 526:108–119, 2014) and for alignment-free sequence comparison by utilizing a metric based on minimal absent words (Chairungsee and Crochemore in Theoret Comput Sci 450:109–116, 2012). They are also used in molecular biology; for instance, three minimal absent words of the human genome were found to play a functional role in a coding region in Ebola virus genomes (Silva et al. in Bioinformatics 31:2421–2425, 2015). In this article we introduce a new application of minimal absent words for on-line pattern matching. Specifically, we present an algorithm that, given a pattern x and a text y, computes the distance between x and every window of size |x| on y. The running time is O(σ|y|)O(σ|y|) , where σσ is the size of the alphabet. Along the way, we show an O(σ|y|)O(σ|y|) -time and O(σ|x|)O(σ|x|) -space algorithm to compute the minimal absent words of every window of size |x| on y, together with some new combinatorial insight on minimal absent words

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Section: Introductionmentioning

confidence: 99%

Minimal Absent Words in a Sliding Window and Applications to On-Line Pattern Matching

Crochemore

Héliou

Kucherov

et al. 2017

Fundamentals of Computation Theory

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“…As future work, we aim to develop new algorithms dealing with the problem of finding absent words in a set of biological sequences [1,4,10,20].…”

Section: Current and Future Devel-opmentmentioning

confidence: 99%

“…For example, searching rare motifs is an important task to identify absent words in genomic sequences [9,10,20]. Moreover, to identify proteins involved in parasitism, it is important to search the infrequent motifs [19].…”

Section: Introductionmentioning

confidence: 99%

Extraction of Infrequent Simple Motifs from a Finite Set of Sequences using a Lattice Structure

El-Falah¹,

Lecroq²,

Elloumi³

2013

DNAG

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“…Notice that minimal and shortest absent words [18] are not the same; minimal absent words are a superset of shortest absent words [15]. An upper bound on the number of minimal absent words is known to be O(σn) [6,13], where σ is the size of the alphabet.…”

Section: Introductionmentioning

confidence: 99%

Parallelising the Computation of Minimal Absent Words

Barton

Héliou

Mouchard

et al. 2016

Parallel Processing and Applied Mathematics

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International audienceAn 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 (Barton et al., 2014). An implementation of this algorithm was also provided by the authors and is currently the fastest available. In this article, we present a new O(n)-time and O(n)-space algorithm for computing all minimal absent words; it has the desirable property that, given the indexing data structure at hand, the computation of minimal absent words can be executed in parallel. Experimental results show that a mul-tiprocessing implementation of this algorithm can accelerate the overall computation by more than a factor of two compared to state-of-the-art approaches. By excluding the indexing data structure construction time, we show that the implementation achieves near-optimal speed-ups

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Efficient computation of shortest absent words in a genomic sequence

Cited by 23 publications

References 8 publications

Minimal Absent Words in a Sliding Window and Applications to On-Line Pattern Matching

Minimal Absent Words in a Sliding Window and Applications to On-Line Pattern Matching

Extraction of Infrequent Simple Motifs from a Finite Set of Sequences using a Lattice Structure

Parallelising the Computation of Minimal Absent Words

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