Visualization and Characterization of Nucleotide Sequences in Bioinformatics: State-of-Art in the Past and Present

Dmitry A. Zimnyakov orcid
Yury Gagarin State Technical University of Saratov, Russia
Institute for Precision Mechanics and Control Problems of the Russian Academy of Sciences, Saratov, Russia
Saratov State University, Russia

Marina V. Alonova orcid (Login required)
Yury Gagarin State Technical University of Saratov, Russia

Anatoly V. Skripal orcid
Saratov State University, Russia

Onega V. Ulianova orcid
Saratov State University, Russia

Valentina A. Feodorova orcid
Saratov State University, Russia


Paper #8980 received 29 May 2023; revised manuscript received 29 Aug 2023; accepted for publication 29 Aug 2023; published online 21 Nov 2023.

DOI: 10.18287/JBPE23.09.040201

Abstract

The review considers the main trends in the development of the methods for representation and characterization of DNA-associated nucleotide sequences, starting from the key works performed in the nineties of the last century and ending with the current state of the art. The basic principles of algorithms for processing nucleotide sequences and generating representing 2D and 3D objects are discussed in relation to such popular methods as polyline representation (generation of H-, Z-, C-, … curves), chaos game representation, and sequence logo representation. In addition, novel approaches to representation of genetic information using the principles of coherent optical information processing, such as GB speckle technique and polarization mapping, are considered. The discussion is illustrated by the examples of graphic images obtained using the basic algorithms for model nucleotide sequences or sequences borrowed from open sources.

Keywords

nucleotide sequences; graphical imaging; polyline representation; chaos game representation; sequence logo; coherent optical imaging

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