On finding minimal absent words

Pinho, Armando J.; Ferreira, Paulo J. S. G.; Garcia, Sara P.; Rodrigues, João M. O. S.

doi:10.1186/1471-2105-10-137

Cited by 43 publications

(55 citation statements)

References 14 publications

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“…The advantages of pMAW over existing works are as follows. It is (provably) linear-time in the worst case as opposed to the one in [15]. Contrary to the lineartime algorithm in [3], we explicitly compute the LCP-intervals.…”

Section: Computation Of Minimal Absent Wordsmentioning

confidence: 99%

“…We first start by explaining some useful properties from [15] we use in algorithm pMAW. Then we present our algorithm in detail, and, finally, we show how it can be adapted for parallel computing.…”

Section: Algorithm Pmawmentioning

confidence: 99%

“…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%

“…The computation of minimal absent words based on the construction of suffix arrays was considered in [15]; although this algorithm has a linear-time performance in practice, the worst-case time complexity is O(n 2 ). The first O(n)-time and O(n)-space suffix-array-based algorithm was recently presented in [3] to bridge this unpleasant gap.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Computation Of Minimal Absent Wordsmentioning

confidence: 99%

Section: Algorithm Pmawmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Parallelising the Computation of Minimal Absent Words

Barton

Héliou

Mouchard

et al. 2016

Parallel Processing and Applied Mathematics

View full text Add to dashboard Cite

show abstract

“…Na literatura, vetores de sufixo generalizados são utilizados para resolver diferentes problemas, como montagem de genomas [Gonnella e Kurtz, 2012a], identificação de padrões que não ocorrem em um conjunto (word absent) [Pinho et al, 2009], casamento de todos os pares sufixo-prefixo [Ohlebusch e Gog, 2010], identificação de repetições [Arnold e Ohlebusch, 2011], recuperação de informação em documentos [Välimäki e Mäkinen, 2007] e processamento de linguagem natural [Hui et al, 2009], dentre outros.…”

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