Complexity of DNA sequencing by hybridization

Błażewicz, Jacek; Kasprzak, Marta

doi:10.1016/s0304-3975(02)00063-4

Cited by 53 publications

(26 citation statements)

References 11 publications

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“…It should be noted that the decision versions of all of the problems formulated in this chapter are in class P (which is also the case of the classical SBH problems, see [3]). However, the search versions of some of them, being the most interesting from the theoretical, as well as practical point of view, are intractable.…”

Section: The Multiplicity Informationmentioning

confidence: 99%

DNA sequencing by hybridization with additional information available

Formanowicz¹

2005

CMST

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Abstract:In classical DNA sequencing by hybridization it is assumed that the information obtained in the biochemical stage of the method is a set of the l-tuples composing the target sequence. It means that the information concerning the number of the repeated l-tuples is not available. Such an assumption was justified by the DNA chip technology constraints. However, nowadays some approximate information about l-tuple multiplicities can be obtained in the experiments, where DNA chips are used. It was a motivation for formulating combinatorial problems which arise when such additional information is taken into account. The goal of this paper is to formulate and classify these problems, what should establish a good starting point for further research concerning algorithmic methods solving DNA sequencing problems with multiplicity information. Moreover, the computational complexity of the new problems is determined, which in most cases is analogous to the complexity of their classical counterparts.

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Section: The Multiplicity Informationmentioning

confidence: 99%

DNA sequencing by hybridization with additional information available

Formanowicz¹

2005

CMST

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“…The existence of errors in the input spectrum makes the problem of reconstructing the original sequence an NP-hard problem [4]. Missing fragments from the experiment turn the problem into the problem of finding the Most-Likely sequence [4].…”

Section: Preliminariesmentioning

confidence: 99%

“…Missing fragments from the experiment turn the problem into the problem of finding the Most-Likely sequence [4]. The most likely sequence is the shortest one containing almost each fragment as a substring.…”

Section: Preliminariesmentioning

confidence: 99%

“…If a spectrum contains all possible fragments of length l of a DNA sequence and there are no errors in the fragments then there exist efficient algorithms for reconstructing the original DNA sequence from the spectrum. In general, however, there are errors in the spectrum, e.g., missing fragments or erroneous fragments, making the problem of reconstructing the original DNA sequence an NP-hard problem [4].…”

Section: Introductionmentioning

confidence: 99%

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An Enhanced Genetic Algorithm for DNA Sequencing by Hybridization with Positive and Negative Errors

Bui

Youssef

2004

Genetic and Evolutionary Computation – GECCO 2004

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Abstract. This paper describes a genetic algorithm for the DNA sequencing problem. The algorithm allows the input spectrum to contain both positive and negative errors as could be expected from a hybridization experiment. The main features of the algorithm include a preprocessing step that reduces the size of the input spectrum and an efficient local optimization. In experimental tests, the algorithm performed very well against existing algorithms. The algorithm also performed very well on a large data set generated in this paper from real genomes data.

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“…The computational problem often used to model this process of DNA fragment assembly is SCSP. A more detailed information about the relation of SBH to SCSP is given in [1], and a novel and promising application of SBH to resequencing is described in [15]. Third, SCSP is also applied in data compression schemes.…”

Section: The Problemmentioning

confidence: 99%

A tissue P system and a DNA microfluidic device for solving the shortest common superstring problem

2004

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Abstract. This paper describes a tissue P system for solving the Shortest Common Superstring Problem in linear time. This tissue P system is well suited for parallel and distributed implementation using a microfluidic device working with DNA strands. The tP system is not based on the usual brute force generate/test technique applied in DNA computing, but builds the space solution gradually. The possible solutions/superstrings are build step by step through the parallel distributed combination of strings using the overlapping concatenation operation. Moreover, the DNA microfluidic device solves the problem autonomously, without the need of external control or manipulation.

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Complexity of DNA sequencing by hybridization

Cited by 53 publications

References 11 publications

DNA sequencing by hybridization with additional information available

DNA sequencing by hybridization with additional information available

An Enhanced Genetic Algorithm for DNA Sequencing by Hybridization with Positive and Negative Errors

A tissue P system and a DNA microfluidic device for solving the shortest common superstring problem

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