Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries

Błaewicz, Jacek; Formanowicz, Piotr; Kasprzak, Marta; Markiewicz, Wojciech T.; Wiercz, Aleksandra

doi:10.1016/j.compbiolchem.2003.12.002

Cited by 18 publications

(13 citation statements)

References 22 publications

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“…In [50] a new sequencing algorithm for the isothermic oligonucleotide libraries has been introduced, basing on the tabu search approach. The proposed algorithm deals with both types of hybridization errors, the negative and positive ones.…”

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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Section: Isothermic Oligonucleotide Librariesmentioning

confidence: 99%

Computational Aspects of DNA Sequencing by Hybridization – a Survey

Kwarciak¹,

Radom²,

Formanowicz³

2018

CMST

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“…This is a simple form of a tabu search [4]. Two fitness measures are required to capture the hybrid nature of the approach -one that captures the mathematically rigorous definition of a reference set, and one that measures an empirically derived characteristic of the proposed solution.…”

Section: Representation Operators and Settingsmentioning

confidence: 99%

“…To measure the degree to which this occurs the genes are sorted by CAI score and an index is assigned to all genes -the gene with the smallest CAI value will be assigned an index of 0 while the gene with greatest CAI value will be assigned an index of N -1 where N is the number of genes in the genome. The indexes of the reference set genes are summed (IDX's in (4)) and this number is normalized 1-4244-1509-8/07/$25.00 02007 IEEE by the maximum attainable rank-fitness value (5) yielding a value between 0 and 1 representing the degree to which the reference set rises to the top of a sorted (by CAI score) list of genes (6).…”

Section: Rank-fitnessmentioning

confidence: 99%

A Multi-Objective Genetic Algorithm that Employs a Hybrid Approach for Isolating Codon Usage Bias Indicative of Translational Efficiency

Raiford

Krane

Doom

et al. 2007

2007 IEEE 7th International Symposium on BioInformatics and BioEngineering

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Isolation oftranslational efficiency bias can have important applications in gene expression prediction and heterologous protein production. In some genomes the presence of a high GC(AT)-content bias can confound the isolation of translational efficiency bias. In other organisms translational efficiency bias is weak making it difficult to isolate. Described here is a multi-objective genetic algorithm that improves the isolation of translational efficiency bias in Streptomyces coelicolor A3(2) and Pseudomonas aeruginosa PAOI, two organisms shown to have high GC-content and weak translational efficiency bias.

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“…We have recently invented a new assembly algorithm working very well with the data from 454 sequencer [2], but consuming noticeable amount of time. In this algorithm our ideas from previous approaches to DNA sequencing by hybridization were partially applied [3,6]. Now, basing on a series of tests on raw data coming from a real experiment with 454 sequencer, we decided to implement our new algorithm with partial parallelization for GPU.…”

Section: Algorithmmentioning

confidence: 99%

Dna Sequence Assembly Involving an Acyclic Graph Model

Błażewicz¹,

Frohmberg²,

Gawron³

et al. 2013

Foundations of Computing and Decision Sciences

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The problem of DNA sequence assembly is well known for its high complexity. Experimental errors of different kinds present in data and huge sizes of the problem instances make this problem very hard to solve. In order to deal with such data, advanced efficient heuristics must be constructed. Here, we propose a new approach to the sequence assembly problem, modeled as the problem of searching for paths in an acyclic digraph. Since the graph representing an assembly instance is not acyclic in general, it is heuristically transformed into the acyclic form. This approach reduces the time of computations significantly and allows to maintain high quality of produced solutions.

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Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries

Cited by 18 publications

References 22 publications

Computational Aspects of DNA Sequencing by Hybridization – a Survey

Computational Aspects of DNA Sequencing by Hybridization – a Survey

A Multi-Objective Genetic Algorithm that Employs a Hybrid Approach for Isolating Codon Usage Bias Indicative of Translational Efficiency

Dna Sequence Assembly Involving an Acyclic Graph Model

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