The complexity of multiple sequence alignment with SP-score that is a metric

Bonizzoni, Paola; Vedova, Gianluca Della

doi:10.1016/s0304-3975(99)00324-2

Cited by 93 publications

(57 citation statements)

References 8 publications

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“…Em 2001, Bonizzoni e Vedova mostraram que o Problema AVS, em sua versão de decisão,é NP-completo também para uma matriz de pontuação que satisfaz aos axiomas de métrica [1], que era uma questão em aberto até então. Em um artigo posterior [8], Winfried Just mostrou que o problema de alinhar seqüênciasé NPdifícil para uma ampla classe de matrizes de pontuação (que inclui as matrizes do artigo de Bonizzoni e Vedova, conforme mostrado em [2]).…”

Section: Resultados Relacionadosunclassified

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Complexidade de Alinhamento de Seqüências Biológicas

Brito¹

2011

TEMA - Tendências Em Matemática Aplicada E Computacional

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Section: Resultados Relacionadosunclassified

“…Posteriormente, outras demonstrações de que o Problema AVS (em sua versão de decisão)é NP-completo surgiram [1,8]. Para uma demonstração detalhada desses fatos mais recentes, remetemos o leitoràs referências bibliográficas [2].…”

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Complexidade de Alinhamento de Seqüências Biológicas

Brito¹

2011

TEMA - Tendências Em Matemática Aplicada E Computacional

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“…We first review the MSA and WMSA problems. MSA and WMSA have been studied extensively [2,7,11,20]. Let Σ be the set of characters and S = {S 1 , S 2 , .…”

Section: Preliminariesmentioning

confidence: 99%

Approximating Border Length for DNA Microarray Synthesis

Wong

Xin

et al.

Lecture Notes in Computer Science

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Abstract. We study the border minimization problem (BMP), which arises in microarray synthesis to place and embed probes in the array. The synthesis is based on a light-directed chemical process in which unintended illumination may contaminate the quality of the experiments. Border length is a measure of the amount of unintended illumination and the objective of BMP is to find a placement and embedding of probes such that the border length is minimized. The problem is believed to be NP-hard. In this paper we show that BMP admits an O( √ n log 2 n)-approximation, where n is the number of probes to be synthesized. In the case where the placement is given in advance, we show that the problem is O(log 2 n)-approximable. We also study a related problem called agreement maximization problem (AMP). In contrast to BMP, we show that AMP admits a constant approximation even when placement is not given in advance.

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“…In the figure, solid plots refer to Steps 1-3 as presented and give the average value (by itself and plus or minus the standard deviation) of n T over single-sequence suffix-set trees for 10 3 randomly generated sequences. 3 Dashed plots, correspondingly, refer to the alternative version of the tree-constructing algorithm. In all cases, it is clear from the plots' linearity with respect to the two logarithmic scales that, on average, n T depends only polynomially on the sequence's length.…”

Section: A Simple Construction Algorithmmentioning

confidence: 99%

“…It follows from the definition of an alignment that the number of different alignments of a given set of sequences is exponentially large [9,47]; in fact, the multiple sequence alignment problem is known to be NP-hard [62,3,21,29]. Feasible approaches to solve the problem are then all of a heuristic nature, as can be seen in [16,46,10,14,42,2,38,39,11].…”

Section: Introductionmentioning

confidence: 99%

Multiple Sequence Alignment Based on Set Covers

Porto

Barbosa

2006

Lecture Notes in Computer Science

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We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the sequences to be aligned. These blocks are obtained with the aid of a new data structure, called a suffix-set tree, which is constructed from the input sequences with the guidance of the residue-alphabet set cover and generalizes the well-known suffix tree of the sequence set. We provide performance results on selected BAliBASE amino-acid sequences and compare them with those yielded by some prominent approaches.

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The complexity of multiple sequence alignment with SP-score that is a metric

Cited by 93 publications

References 8 publications

Complexidade de Alinhamento de Seqüências Biológicas

Complexidade de Alinhamento de Seqüências Biológicas

Approximating Border Length for DNA Microarray Synthesis

Multiple Sequence Alignment Based on Set Covers

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