A greedy algorithm for the DNA sequencing by hybridization with positive and negative errors and information about repetitions

Kwarciak, K.; Formanowicz, Piotr

doi:10.2478/v10175-011-0015-0

Cited by 5 publications

(5 citation statements)

References 6 publications

(10 reference statements)

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“…In our algorithm, we assume no knowledge about the number of times when different fragments hybridized with the same probe. There are articles dealing with such a problem, for example [ 16 – 18 ], but in our approach, we consider negative errors from repetitions as missing data.…”

Section: Methodsmentioning

confidence: 99%

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An Algorithm for Sequencing by Hybridization Based on an Alternating DNA Chip

Radom

Formanowicz

2017

Interdiscip Sci Comput Life Sci

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Sequencing by hybridization allows the reconstruction of the DNA string of a given length from smaller fragments. These fragments are obtained in the hybridization experiment in which the DNA hybridizes to a DNA chip. In a classical approach, the chip consists of all oligonucleotides of a given length, with only one type of oligonucleotide for each probe of the chip. In this paper, we propose an algorithm solving the non-classical case of SBH, where the chip probes consist set of oligonucleotides described by some specific pattern. We will present the definition of such a non-classical DNA chip and the algorithm solving a sequencing problem related to such a chip. Unlike recent metaheuristic approaches to the classical SBH problem, the proposed algorithm tries to find an exact sequence, and even in the presence of all the hybridization errors in spectrum is very often able to do so in a short time. If only negative errors from repetitions are allowed, then the algorithm is able to reconstruct sequences having length of thousands nucleotides.

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Section: Methodsmentioning

confidence: 99%

“…In the most recent paper concerning SBH method, an approach has been presented based on the limited knowledge how many times an oligonucleotide from the probe is present in the target DNA, i.e., once or more. Knowing that simple fact can greatly improve the method, as shown in [ 16 – 18 ].…”

Section: Introductionmentioning

confidence: 99%

An Algorithm for Sequencing by Hybridization Based on an Alternating DNA Chip

Radom

Formanowicz

2017

Interdiscip Sci Comput Life Sci

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“…One exact algorithm has been proposed: a branch and bound method [26] which solves the problem optimally. The implementation takes into consideration negative errors of arbitrary types and the multiplicity information model of the type "one and many".…”

Section: 1 Branch and Bound Algorithmmentioning

confidence: 99%

“…Another implemented algorithm is a greedy heuristic for SBH with errors of arbitrary types [27]. It is able to use as an input a multispectrum with multiplicity information of the type "one and many" or "one, two and many"…”

Section: 2 Greedy Algorithmmentioning

confidence: 99%

Computational Aspects of DNA Sequencing by Hybridization – a Survey

Kwarciak¹,

Radom²,

Formanowicz³

2018

CMST

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Sequencing by hybridization (SBH) is a method of reading DNA sequence from its smaller fragments. Such a method has been proposed in late 1980s and until the emergence of the new generation sequencing it has been widely used and improved. Since the initial, classical approach to SBH, many modifications and enhancements was proposed, aimed at improving the preciseness and the length of sequences which can be unambiguously read. Even now, for some DNA sequences sequencing by hybridization can still be used effectively and at a low cost. In this paper many different approaches to the SBH will be described, mainly from the points of view of algorithms and computational complexity.

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“…[8]), or DNA assembly (see e.g. [9] and [10]). Moreover, these problems apart from the alignment score require the alignment itself to be computed as well.…”

Section: Introductionmentioning

confidence: 99%

G-PAS 2.0 – an improved version of protein alignment tool with an efficient backtracking routine on multiple GPUs

Frohmberg¹,

Kierzynka²,

Błażewicz³

et al. 2012

Bulletin of the Polish Academy of Sciences: Technical Sciences

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Several highly efficient alignment tools have been released over the past few years, including those taking advantage of GPUs (Graphics Processing Units). G-PAS (GPU-based Pairwise Alignment Software) was one of them, however, with a couple of interesting features that made it unique. Nevertheless, in order to adapt it to a new computational architecture some changes had to be introduced. In this paper we present G-PAS 2.0 - a new version of the software for performing high-throughput alignment. Results show, that the new version is faster nearly by a fourth on the same hardware, reaching over 20 GCUPS (Giga Cell Updates Per Second).

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A greedy algorithm for the DNA sequencing by hybridization with positive and negative errors and information about repetitions

Cited by 5 publications

References 6 publications

An Algorithm for Sequencing by Hybridization Based on an Alternating DNA Chip

An Algorithm for Sequencing by Hybridization Based on an Alternating DNA Chip

Computational Aspects of DNA Sequencing by Hybridization – a Survey

G-PAS 2.0 – an improved version of protein alignment tool with an efficient backtracking routine on multiple GPUs

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