Using the Davey-MacKay code construction for barcodes in DNA sequencing

Kracht, David; Schober, Steffen

doi:10.1109/istc.2014.6955102

Cited by 7 publications

(6 citation statements)

References 5 publications

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“…The Chi-Squared test is a non-parametric test that is used to determine if the observed data is significantly different from expected data and is calculated using Equation (A. 1) where k is the number of data samples, o i is the observed data at sample i and e i is the expected value of the ith sample [25], [26], [27].…”

Section: A Performance Metrics For Analysis and Methodologymentioning

confidence: 99%

Symbol-Level Synchronisation Channel Modelling With Real-World Application: From Davey-Mackay, Fritchman to Markov

Achari¹,

Holmes²,

Cheng

2021

Preprint

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Errors in realistic channels contain not only substitution errors, but synchronisation errors as well. Moreover, these errors are rarely statistically independent in nature. By extending on the idea of the Fritchman channel model, a novel error category-based methodology in determining channel characteristics is described for memory channels which contain insertion, deletion, and substitution errors.The practicality of such a methodology is reinforced by making use of real communication data from a visible light communication system. Simulation results show that the error-free and error runs using this new method of defining the channel clearly deviates from the Davey-Mackay synchronisation model which is memoryless in nature. This further emphasises the inherent memory in these synchronisation channels which we are now able to characterise. Additionally, a new method to determine the parameters of a synchronisation memory channel using the Levenshtein distance metric is detailed. This method of channel modelling allows for more realistic communication models to be simulated and can easily extend to other areas of research such as DNA barcoding in the medical domain.

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Section: A Performance Metrics For Analysis and Methodologymentioning

confidence: 99%

Symbol-Level Synchronisation Channel Modelling With Real-World Application: From Davey-Mackay, Fritchman to Markov

Achari¹,

Holmes²,

Cheng

2021

Preprint

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“…The main concepts presented in this section originates from the ideas first given by Davey and MacKay [ 20 ]. The fact, that quaternary watermark codes can be applied for DNA sequencing was preliminary outlined in [ 23 ], but sequence constraint on practical oligonucleotides can not be found in this conference paper. Let us denote some basic facts about barcodes first and postpone specific sequence constraints to the section about reasonable encoder settings.…”

Section: Methodsmentioning

confidence: 99%

Insertion and deletion correcting DNA barcodes based on watermarks

Kracht

Schober

2015

BMC Bioinformatics

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BackgroundBarcode multiplexing is a key strategy for sharing the rising capacity of next-generation sequencing devices: Synthetic DNA tags, called barcodes, are attached to natural DNA fragments within the library preparation procedure. Different libraries, can individually be labeled with barcodes for a joint sequencing procedure. A post-processing step is needed to sort the sequencing data according to their origin, utilizing these DNA labels. The final separation step is called demultiplexing and is mainly determined by the characteristics of the DNA code words used as labels.Currently, we are facing two different strategies for barcoding: One is based on the Hamming distance, the other uses the edit metric to measure distances of code words. The theory of channel coding provides well-known code constructions for Hamming metric. They provide a large number of code words with variable lengths and maximal correction capability regarding substitution errors. However, some sequencing platforms are known to have exceptional high numbers of insertion or deletion errors. Barcodes based on the edit distance can take insertion and deletion errors into account in the decoding process. Unfortunately, there is no explicit code-construction known that gives optimal codes for edit metric.ResultsIn the present work we focus on an entirely different perspective to obtain DNA barcodes. We consider a concatenated code construction, producing so-called watermark codes, which were first proposed by Davey and Mackay, to communicate via binary channels with synchronization errors. We adapt and extend the concepts of watermark codes to use them for DNA sequencing. Moreover, we provide an exemplary set of barcodes that are experimentally compatible with common next-generation sequencing platforms. Finally, a realistic simulation scenario is use to evaluate the proposed codes to show that the watermark concept is suitable for DNA sequencing applications.ConclusionOur adaption of watermark codes enables the construction of barcodes that are capable of correcting substitutions, insertion and deletion errors. The presented approach has the advantage of not needing any markers or technical sequences to recover the position of the barcode in the sequencing reads, which poses a significant restriction with other approaches.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0482-7) contains supplementary material, which is available to authorized users.

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“…The DM code construction has been successfully used in many applications ranging from the barcoding of DNA in [3,4] to speech watermarking in [15]. There has also been much work on improving the code construction and decoding, such as [17,18,19].…”

Section: Davey-mackay Synchronisation Channel and Watermark Codementioning

confidence: 99%

“…This impact is already witnessed in prevailing real-world communication systems that use visible light or free-space optics where synchronisation between the receiver and transmitter is not easily maintained and as a result, these systems suffer from synchronisation errors [1,2]. The concern of synchronisation and its related errors are even found in unconventional fields such as DNA sequencing [3,4] to even more intricate specialisations such as molecular communications [5,6]. The latter has gained popularity in recent years as a potential for data communication in nano and micro systems, where open problems in the field contemplate the effects of synchronisation and memory [5,6].…”

Section: Introductionmentioning

confidence: 99%

Watermark-Based Code Construction for Finite-State Markov Channel with Synchronisation Errors

Achari¹,

Liu²

2022

Preprint

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With advancements in telecommunications, data transmission over increasingly harsher channels that produce synchronisation errors is inevitable. Coding schemes for such channels are available through techniques such as the Davey-MacKay watermark coding; however, this is limited to memoryless channel estimates. Memory must be accounted for to ensure a realistic channel approximation -similar to a Finite State Markov Chain or Fritchman Model. A novel code construction and decoder are developed to correct synchronisation errors while considering the channel's correlated memory effects by incorporating ideas from the watermark scheme and memory modelling. Simulation results show that the proposed code construction and decoder rival the first and second-order Davey-MacKay type watermark decoder and even perform slightly better when the inner-channel capacity is higher than 0.9. The proposed system and decoder may prove helpful in fields such as free-space optics and possibly molecular communication, where harsh channels are used for communication.

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Using the Davey-MacKay code construction for barcodes in DNA sequencing

Cited by 7 publications

References 5 publications

Symbol-Level Synchronisation Channel Modelling With Real-World Application: From Davey-Mackay, Fritchman to Markov

Symbol-Level Synchronisation Channel Modelling With Real-World Application: From Davey-Mackay, Fritchman to Markov

Insertion and deletion correcting DNA barcodes based on watermarks

Watermark-Based Code Construction for Finite-State Markov Channel with Synchronisation Errors

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