An error-correcting code framework for genetic sequence analysis

May, Elebeoba; Vouk, Mladen A.; Bitzer, Donald L.; Rosnick, David

doi:10.1016/j.jfranklin.2003.12.009

Cited by 37 publications

(22 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The reader is referred to the paper by Fabris (2009) for a critical review and summary of earlier work and formulation of the information theory framework for various related problems. Some other works study the problem from purely coding theory point of view and try to discover hidden coding structures (May et al, 2004;Battail, 2004). Only a few works (Gong et al, 2011;Balado, 2013), however, attempted at a full analysis of the information transfer processes in the genome such as protein coding, to derive its fundamental limits.…”

Section: Introductionmentioning

confidence: 99%

The information capacity of the genetic code: Is the natural code optimal?

Kuruoğlu

Arndt

2017

Journal of Theoretical Biology

View full text Add to dashboard Cite

A B S T R A C TWe envision the molecular evolution process as an information transfer process and provide a quantitative measure for information preservation in terms of the channel capacity according to the channel coding theorem of Shannon. We calculate Information capacities of DNA on the nucleotide (for non-coding DNA) and the amino acid (for coding DNA) level using various substitution models. We extend our results on coding DNA to a discussion about the optimality of the natural codon-amino acid code. We provide the results of an adaptive search algorithm in the code domain and demonstrate the existence of a large number of genetic codes with higher information capacity. Our results support the hypothesis of an ancient extension from a 2-nucleotide codon to the current 3-nucleotide codon code to encode the various amino acids.

show abstract

Section: Introductionmentioning

confidence: 99%

The information capacity of the genetic code: Is the natural code optimal?

Kuruoğlu

Arndt

2017

Journal of Theoretical Biology

View full text Add to dashboard Cite

show abstract

“…In this model, we assume that mutations can also occur in the involved proteins, that is RNA polymerase, ribosome and tRNA. Other similar models for gene expression are summarised in Reference [6].…”

Section: Analogies and Modellingmentioning

confidence: 99%

“…Moreover, it might help in discovering new facts that allow further understanding of these processes. The work of May [6] established the first concrete ideas for modelling gene expression interactions based on algorithms inspired from coding theory. The process of translation in prokaryotes is triggered by the detection of a biological sync word known as the SD sequence which is located around 10 bases before the translation start codon AUG.…”

Section: Channel Coding For Modelling Gene Expressionmentioning

confidence: 99%

“…Battail [4] argued about the existence of nested error correcting codes in the DNA supported by several biological observations such as the size of the human genome being far larger than the size needed to specify every characteristic of any given individual. On other fronts, Mac Donaill [5] proposed a parity check code interpretation of nucleotide composition, and May et al [6] proposed the use of block and convolutional codes to model the process of translation initiation in prokaryotic organisms. This paper is organised as follows.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

On genomic coding theory

Dawy¹,

Hanus²,

Weindl³

et al. 2007

Trans Emerging Tel Tech

View full text Add to dashboard Cite

SUMMARYThis paper gives a brief overview of several applications from the emerging interdisciplinary field of genomic coding theory that aims at applying concepts and techniques from the field of coding theory to problems from the field of molecular biology. This is motivated by the high precision and robustness found in genomic processes in addition to the increase in the availability of genomic data for a wide range of species. The considered applications include source coding for DNA classification, channel coding for modelling gene expression with emphasis on the process of translation, existence of error correcting codes in the DNA and channel coding structure in the genetic code. Example results are presented that demonstrate the relevance of the proposed approaches and open questions are formulated to suggest future research work.

show abstract

“…[2,8,9] On the other hand, the rapid increase in genetic data has spurred a renewed interest to use concepts and tools from the field of communication engineering to analyze and understand various processes in the field of molecular biology. [10][11][12][13][14][15][16] According to the points Battail proposed, [10,11] 124 X. Liu et al proofreading does not correct errors present in the original genetic message.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Similarity/Dissimilarity of DNA Sequences Based on Convolutional Code Model

Xiao

Tian

Wang

2010

Nucleosides, Nucleotides & Nucleic Acids

View full text Add to dashboard Cite

Based on the convolutional code model of error-correction coding theory, we propose an approach to characterize and compare DNA sequences with consideration of the effect of codon context. We construct an 8-component vector whose components are the normalized leading eigenvalues of the L/L and M/M matrices associated with the original DNA sequences and the transformed sequences. The utility of our approach is illustrated by the examination of the similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of 11 species, and the efficiency of error-correction coding theory in analysis of similarity/dissimilarity of DNA sequences is represented.

show abstract

An error-correcting code framework for genetic sequence analysis

Cited by 37 publications

References 54 publications

The information capacity of the genetic code: Is the natural code optimal?

The information capacity of the genetic code: Is the natural code optimal?

On genomic coding theory

Analysis of Similarity/Dissimilarity of DNA Sequences Based on Convolutional Code Model

Contact Info

Product

Resources

About