Multistage isothermic sequencing by hybridization

Błaewicz, Jacek; Formanowicz, Piotr

doi:10.1016/j.compbiolchem.2004.12.001

Cited by 3 publications

(3 citation statements)

References 15 publications

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“…An interesting approach has been introduced in [51]. It joins isothermic libraries with a method described earlier: the multistage hybridization.…”

Section: Isothermic Oligonucleotide Librariesmentioning

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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“…An interesting approach has been introduced in [51]. It joins isothermic libraries with a method described earlier: the multistage hybridization.…”

Section: Isothermic Oligonucleotide Librariesmentioning

confidence: 99%

Computational Aspects of DNA Sequencing by Hybridization – a Survey

Kwarciak¹,

Radom²,

Formanowicz³

2018

CMST

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“…One of the enhancements introduced an additional information to the spectrum, i.e., estimated location in the target sequence for each of its elements [ 6 – 8 ]. One can here mention interactive protocols also known as sequencing in rounds [ 9 – 11 ]. This approach is still being improved, creating some new open questions, e.g., for the minimal number of rounds required for a given DNA to be successfully read [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

“…This approach is still being improved, creating some new open questions, e.g., for the minimal number of rounds required for a given DNA to be successfully read [ 12 ]. Another way of improving SBH method is the isothermic libraries [ 9 , 13 , 14 ], where specially designed oligonucleotide libraries that dependent on the melting temperature are being used in the probes of the microarray. There are also recent enhancements, for example, an approach that deals with the repetitive subsequences in the target sequence [ 15 ].…”

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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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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