DNA Sequence Design Based on Template Strategy.

Liu, Wenbin; Wang, Shudong; Gao, Lin; Zhang, Fengyue; Xu, Jin

doi:10.1002/chin.200405241

Cited by 5 publications

(6 citation statements)

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“…For optimization of the GC content previously published strategies can be applied [12] , [13] . These schemes however, operate in a binary format, therefore for short sequences coding efficiency is low.…”

Section: Resultsmentioning

confidence: 99%

“…Their designs could be easily replaced by Hamming (6,3) or Hamming (6,2) quaternary codes ( Tables 3 , 4 ) providing more robust minimal distance, minimize sequence redundancy and achieve more tags than presented both by Epicentre and Illumina together. Early designs of barcodes used for DNA microarray provide interesting algorithms with sufficient minimal distance and error correcting capacity [11] , [13] , yet they were made for longer, microarray type of oligonucleotides and were left unused in recent publications. Currently, multiplex parallel sequencing is steadily growing in its diversity and extent of application.…”

Section: Discussionmentioning

confidence: 99%

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Generalized DNA Barcode Design Based on Hamming Codes

Bystrykh

2012

PLoS ONE

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The diversity and scope of multiplex parallel sequencing applications is steadily increasing. Critically, multiplex parallel sequencing applications methods rely on the use of barcoded primers for sample identification, and the quality of the barcodes directly impacts the quality of the resulting sequence data. Inspection of the recent publications reveals a surprisingly variable quality of the barcodes employed. Some barcodes are made in a semi empirical fashion, without quantitative consideration of error correction or minimal distance properties. After systematic comparison of published barcode sets, including commercially distributed barcoded primers from Illumina and Epicentre, methods for improved, Hamming code-based sequences are suggested and illustrated. Hamming barcodes can be employed for DNA tag designs in many different ways while preserving minimal distance and error-correcting properties. In addition, Hamming barcodes remain flexible with regard to essential biological parameters such as sequence redundancy and GC content. Wider adoption of improved Hamming barcodes is encouraged in multiplex parallel sequencing applications.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Generalized DNA Barcode Design Based on Hamming Codes

Bystrykh

2012

PLoS ONE

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“…), an application for DNA studies was far from successful. A few authors rediscovered Hamming code while making a theory of oligonucleotide design for microarrays [ 28 , 29 ]. This however was not implemented in commercially available microarrays.…”

Section: Discussionmentioning

confidence: 99%

Levenshtein error-correcting barcodes for multiplexed DNA sequencing

2013

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BackgroundHigh-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called multiplexing approach relies on a specific DNA tag or barcode that is attached to the sequencing or amplification primer and hence appears at the beginning of the sequence in every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence.Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and Levenshtein codes.ResultLevenshtein codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this paper we demonstrate the decreased error correction capability of Levenshtein codes in a DNA context and suggest an adaptation of Levenshtein codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaption we take the DNA context into account and redefine the word length whenever an insertion or deletion is revealed. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors.ConclusionWe present an adaptation of Levenshtein codes to DNA contexts capable of correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of recovering the new length of the corrupted codeword and of correcting on average more random mutations than traditional Levenshtein or Hamming codes.As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance.

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“…The simplest and most representative algorithm is exhaustive methods and random search algorithms [12], [13], but they are not very efficient because of using a lot of computer resources. Template mapping strategies [14], [15] were used to select dissimilar codes among numerous DNA codes. A directed graph is used by Feldkamp to design DNA codes [16].…”

Section: Introductionmentioning

confidence: 99%

A BPSON Algorithm Applied to DNA Codes Design

Liu

Wang

et al. 2019

IEEE Access

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DNA computing proposed by Adelman is new biotechnology which provides a new way to solve NP-hard problem. It has a promising future and successful results of various applications. DNA codes design is a significant step in DNA computing. Therefore, reliable DNA codes design not only can avoid non-specific hybridization between a code and its Watson-Crick complement but also can improve the efficiency of DNA computing. In this paper, a new algorithm is proposed to design reliable DNA codes. This algorithm combines the Bat algorithm and PSO algorithm. Fast nondominated sorting is used to assign a rank for codes. Thus, it is called BPSON for short. A bat algorithm is used to overcome PSO fall into the local optimal solution and enhance global search ability. In addition, for the purpose of verifying the effectiveness of our algorithm, the performance of BPSON is compared with the previous works. The experimental results show that codes obtained by our algorithm can avoid the appearance of secondary structure, which is beneficial to the specific hybridization among codes and has better thermodynamic properties. The results show that our algorithm can provide optimal codes for DNA computing.INDEX TERMS BPSON algorithm, DNA computing, DNA codes design, fast nondominated sort.

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DNA Sequence Design Based on Template Strategy.

Cited by 5 publications

References 1 publication

Generalized DNA Barcode Design Based on Hamming Codes

Generalized DNA Barcode Design Based on Hamming Codes

Levenshtein error-correcting barcodes for multiplexed DNA sequencing

A BPSON Algorithm Applied to DNA Codes Design

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