On genomic coding theory

Dawy, Zaher; Hanus, P.; Weindl, Johanna; Dingel, J.; Morcos, Faruck

doi:10.1002/ett.1201

Cited by 11 publications

(8 citation statements)

References 15 publications

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“…We describe here an open problem to be confronted by the application of coding theory, a means of estimating the code-words that would maximize error control in an epigenomic communication system (see [ 42 ] for a brief overview). Digital signal processing (DSP) provides the tools to analyze genome-wide regulatory features of such an epigenomic signal [ 43 ].…”

Section: Discussionmentioning

confidence: 99%

Information Thermodynamics of Cytosine DNA Methylation

Sanchez

Mackenzie

2016

PLoS ONE

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Cytosine DNA methylation (CDM) is a stable epigenetic modification to the genome and a widespread regulatory process in living organisms that involves multicomponent molecular machines. Genome-wide cytosine methylation patterning participates in the epigenetic reprogramming of a cell, suggesting that the biological information contained within methylation positions may be amenable to decoding. Adaptation to a new cellular or organismal environment also implies the potential for genome-wide redistribution of CDM changes that will ensure the stability of DNA molecules. This raises the question of whether or not we would be able to sort out the regulatory methylation signals from the CDM background (“noise”) induced by thermal fluctuations. Here, we propose a novel statistical and information thermodynamic description of the CDM changes to address the last question. The physical basis of our statistical mechanical model was evaluated in two respects: 1) the adherence to Landauer’s principle, according to which molecular machines must dissipate a minimum energy ε = kBT ln2 at each logic operation, where kB is the Boltzmann constant, and T is the absolute temperature and 2) whether or not the binary stretch of methylation marks on the DNA molecule comprise a language of sorts, properly constrained by thermodynamic principles. The study was performed for genome-wide methylation data from 152 ecotypes and 40 trans-generational variations of Arabidopsis thaliana and 93 human tissues. The DNA persistence length, a basic mechanical property altered by CDM, was estimated with values from 39 to 66.9 nm. Classical methylome analysis can be retrieved by applying information thermodynamic modelling, which is able to discriminate signal from noise. Our finding suggests that the CDM signal comprises a language scheme properly constrained by molecular thermodynamic principles, which is part of an epigenomic communication system that obeys the same thermodynamic rules as do current human communication systems.

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Section: Discussionmentioning

confidence: 99%

Information Thermodynamics of Cytosine DNA Methylation

Sanchez

Mackenzie

2016

PLoS ONE

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“…In (6.10), R G denotes the code rate of the global regular code, which is R G ¼ 1 À W/n. This GLDPC code design is quite suitable for code-rate adaptation, as almost continuous tuning of the code rate is possible by simply varying the parameter d. In addition to channel coding, the source coding principles have also been used to compress genomic sequences by taking their structural properties into account [12,16].…”

Section: Mà1 Vtmentioning

confidence: 99%

Classical and Quantum Error-Correction Coding in Genetics

Djordjević

2016

Quantum Biological Information Theory

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The subject of this chapter is the use of classical/quantum information theory and coding in genetics and evolution. The chapter starts with the description of using the concepts from both classical and quantum information theories to describe the evolution of biological channel capacity through generations. In order to do so, several classical and quantum biological channel models are employed including the Markovian classical and Markovian-like quantum model, hybrid quantum-classical model, multilevel symmetric channel model, and Kimura model-based Markovian process. In order to describe the reliable long-time storage of genetic information in DNA, the use of unequal error protection (UEP) coding is studied. Several classes of error-correction codes suitable for UEP on a cellular level are described including nested coding, multilevel coding (MLC), rateadaptive coding, and generalized LDPC coding. The use of concepts of constrained coding to describe the genetic information flow from DNA to proteins is also described as well as joint-constrained and error-correction coding. After that, the use of quantum error-correction concepts to deal with environmental errors including canonical quantum error-correction and stabilizer codes is briefly described. One particular class of stabilizer codes, known as topological codes, is then described that might be relevant to biological processes as they only involve the local qubits in encoding process. Another relevant class of codes, the subsystem codes, is then described. The key idea behind subsystem codes is to decompose the quantum code as the tensor product of two subsystems, exon subsystem A and intron subsystem B, and we are concerned with correcting errors only on the exon subsystem. Finally, we describe the use of nonbinary quantum stabilizer codes to deal with nucleobase substitution errors, both random and burst errors. We also briefly discuss the possible use of both classical and quantum error-correction concepts to improve tolerance to tumor and cancer introducing errors.

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“…In biological communication system, after transcription and translation phase the information in DNA is transformed into proteins [9]. In transcription, the double stranded DNA molecule is used to synthesize a new single stranded molecule called messenger RNA (mRNA).…”

Section: Central Dogma Of Molecular Biologymentioning

confidence: 99%

“…The resulting mRNA is consequently spliced to remove the introns (non-coding regions) which results in a sequence of pure exons called mature mRNA. The mature mRNA travels in the cell until the ribosome binds to it at a specific region in order to start the process of translation [9]. Once the ribosome binds properly (translation initiation), it starts processing triplets of bases (also called codons) of the mature mRNA to produce amino acids.…”

Section: Central Dogma Of Molecular Biologymentioning

confidence: 99%

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Error encoding and decoding model over communication channel for synthesis of proteins from DNA sequences

Debata

Das

Mishra

et al. 2012

Proceedings of the International Conference on Advances in Computing, Communications and Informatics

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The expression 'error correcting code' can be understood as a code with the ability to detect and correct the presence of errors caused by noise or other impairments or mutations during transmission from the transmitter/nucleus to the receiver/organelle. It has the additional ability to reconstruct the error free original data. To check the error in information digits many error detecting and correcting codes have been developed. The main aim of these error correcting codes is to encode the information digits and decode these digits to correct the common errors in transmission. This information theory helps to study the information transmission in biological systems and extend the field of coding theory into the biological domain. In the cellular level, the information in DNA is transformed into proteins. The sequence of bases like Adenine (A), Thymine (T), Guanine (G) and Cytosine (C) in deoxyribonucleic acid (DNA) may be considered as digital codes which transmit genetic information. This paper shows the existence of an error correcting code in the DNA structure, by encoding the DNA sequences using Reed-Muller error correcting code.

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On genomic coding theory

Cited by 11 publications

References 15 publications

Information Thermodynamics of Cytosine DNA Methylation

Information Thermodynamics of Cytosine DNA Methylation

Classical and Quantum Error-Correction Coding in Genetics

Error encoding and decoding model over communication channel for synthesis of proteins from DNA sequences

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