Optimizing restriction site placement for synthetic genomes

Montes, Pablo; Memelli, Heraldo; Ward, Charles B.; Kim, Sangho; Mitchell, Joseph S. B.; Skiena, Steven

doi:10.1016/j.ic.2012.02.003

Cited by 4 publications

(3 citation statements)

References 17 publications

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“…He suggests a dynamic programming algorithm that is exponential in the length of the longest restriction site and proves that the problem is NP-complete for non-fixed restriction site lengths. Another related problem is the Unique Restriction Site Placement Problem (URSPP) presented in [19]. The objective in this problem is to allow only one restriction site for any given restriction enzyme, keep the translated sequence of amino acids unchanged, and minimize the maximum gap between adjacent restriction sites.…”

Section: Theoretical Analysis Of Related Problemsmentioning

confidence: 99%

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Eliminating unwanted patterns with minimal interference

Leibovich,

Gronau

2021

Preprint

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Section: Theoretical Analysis Of Related Problemsmentioning

confidence: 99%

“…They do not provide a detailed description of their algorithm and specifically how they avoid creating new restriction sites. Both [23] and [19] give higher priority to avoiding changes in the translated amino acid sequence over the number or placement of restriction sites.…”

Section: Theoretical Analysis Of Related Problemsmentioning

confidence: 99%

Eliminating unwanted patterns with minimal interference

Leibovich,

Gronau

2021

Preprint

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“…Restriction site and other pattern placement/elimination is an NP-hard problem in its general form (Montes et al, 2010 ). Because most patterns have sufficient length to occur sparsely by chance, in conjunction with the small number of patterns that are usually targeted when designing genes, the problem of incorporating and eliminating patterns becomes trivial, and as a singular objective it has a linear time complexity as a function of sequence length.…”

Section: Gene Design Objectives and Algorithmsmentioning

confidence: 99%

Computational Tools and Algorithms for Designing Customized Synthetic Genes

Gould

Hendy

Papamichail

2014

Front. Bioeng. Biotechnol.

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Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein-coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review, we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.

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Optimal Design of Synthetic DNA Sequences Without Unwanted Binding Sites

Gronau¹

2022

Journal of Computational Biology

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Optimizing restriction site placement for synthetic genomes

Cited by 4 publications

References 17 publications

Eliminating unwanted patterns with minimal interference

Eliminating unwanted patterns with minimal interference

Computational Tools and Algorithms for Designing Customized Synthetic Genes

Optimal Design of Synthetic DNA Sequences Without Unwanted Binding Sites

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