Applying Techniques from Frame Synchronization for Biological Sequence Analysis

Weindl, Johanna; Hagenauer, J.

doi:10.1109/icc.2007.142

Cited by 10 publications

(4 citation statements)

References 11 publications

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“…This procedure is similar to the serial acquisition of sync markers in synchronous transport systems. Synchronization has been mostly analyzed in relation to Escherichia coli bacteria, which is the simplest case [57][58][59][60].…”

Section: Synchronizationmentioning

confidence: 99%

Information Theory, Living Systems, and Communication Engineering

Bajić

2024

Entropy

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Mainstream research on information theory within the field of living systems involves the application of analytical tools to understand a broad range of life processes. This paper is dedicated to an opposite problem: it explores the information theory and communication engineering methods that have counterparts in the data transmission process by way of DNA structures and neural fibers. Considering the requirements of modern multimedia, transmission methods chosen by nature may be different, suboptimal, or even far from optimal. However, nature is known for rational resource usage, so its methods have a significant advantage: they are proven to be sustainable. Perhaps understanding the engineering aspects of methods of nature can inspire a design of alternative green, stable, and low-cost transmission.

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Section: Synchronizationmentioning

confidence: 99%

Information Theory, Living Systems, and Communication Engineering

Bajić

2024

Entropy

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“…Frame synchronization method is not only used in digital communication systems but also in gene expression as shown by Weindl and Hagenauer (2007). In fixed sequences, the gene uses a fixed sequence to sign the fundamental expression first (Levy & Yaakobi, 2017).…”

Section: Introductionmentioning

confidence: 99%

Maximality on Construction of Ternary Cross Bifix Free Code

Affaf

2019

ComTech

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The purpose of this research was to show that ternary cross bifix free code CBFS3(2m+1) and CBFS3(2m+2) achieved the maximum for every natural number m. This research was a literature review. A cross bifix free codes was constructed by using Dyck path method which achieved the maximality, that was non-expandable on binary set sequences for appropriate length. This result is obtained by partitioning members of CBFS3(2m+1) and CBFS3(2m+2) and comparing them with the maximality of CBFS2(2m+1) and CBFS2(2m+2). For small length 3, the result also shows that the code CBFS3(3) is optimal.

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“…From the bioinformatics point of view, the design of efficient algorithms for frameshift detection can improve the performance of the assembly process, decrease requirements on the sequencing coverage and reduce the cost of sequencing. See also Kislyuk et al [29] and references therein, for approaches from a bioinformatics point of view, and Weindl & Hagenauer [30] for a communication theory approach. Another important applicative aspect is related to the detection of programmed frameshifts.…”

Section: Frame Synchronization As a Classification Problemmentioning

confidence: 99%

DNA, dichotomic classes and frame synchronization: a quasi-crystal framework

Giannerini

González

Rosa

2012

Phil. Trans. R. Soc. A.

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In this article, we show how a new mathematical model of the genetic code can be exploited for investigating the almost periodic properties of DNA and mRNA protein-coding sequences. We present the main mathematical features of the model and highlight its connections with both number theory and group theory. The group theoretic framework presents interesting analogies with the theory of crystals. Moreover, we exploit the information provided by dichotomic classes, binary variables naturally derived from the mathematical model, in order to build statistical classifiers for retrieving and predicting the normal reading frame used by the ribosome in protein synthesis. The results show that coding sequences possess a local informational structure that can be related to frame synchronization processes. The information for retrieving the normal reading frame, which implies the existence of short-range correlations and almost periodic structures related to the organization of codons, offers an interesting analogy with the properties of quasi-crystals. From a theoretical point of view, our results might contribute to clarifying the relation between biological information and shape in nucleic acids and proteins. Also, from the point of view of applications, we present new promising tools for designing efficient algorithms for frame synchronization, which plays a crucial role in faithful synthesis of proteins.

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Applying Techniques from Frame Synchronization for Biological Sequence Analysis

Cited by 10 publications

References 11 publications

Information Theory, Living Systems, and Communication Engineering

Information Theory, Living Systems, and Communication Engineering

Maximality on Construction of Ternary Cross Bifix Free Code

DNA, dichotomic classes and frame synchronization: a quasi-crystal framework

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