A degeneration-reducing criterion for optimal digital mapping of genetic codes

A degeneration-reducing criterion for optimal digital mapping of genetic codes

Článek WoS

Bioinformatics may seem to be a scientific field processing primarily large string datasets, as nucleotides and amino acids are represented with dedicated characters. On the other hand, many computational tasks that bioinformatics challenges are mathematical problems understandable as operations with digits. In fact, many computational tasks are solved this way in the background. One of the most widely used digital representations is mapping of nucleotides and amino acids with integers 0–3 and 0–20, respectively. The limitation of this mapping occurs when the digital signal of nucleotides has to be translated into a digital signal of amino acids as the genetic code is degenerated. This causes non-monotonies in a mapping function. Although map for reducing this undesirable effect has already been proposed, it is defined theoretically and for standard genetic codes only. In this study, we derived a novel optimal criterion for reducing the influence of degeneration by utilizing a large dataset of real sequences with various genetic codes. As a result, we proposed a new robust global optimal map suitable for any genetic code as well as specialized optimal maps for particular genetic codes.

Bioinformatics may seem to be a scientific field processing primarily large string datasets, as nucleotides and amino acids are represented with dedicated characters. On the other hand, many computational tasks that bioinformatics challenges are mathematical problems understandable as operations with digits. In fact, many computational tasks are solved this way in the background. One of the most widely used digital representations is mapping of nucleotides and amino acids with integers 0–3 and 0–20, respectively. The limitation of this mapping occurs when the digital signal of nucleotides has to be translated into a digital signal of amino acids as the genetic code is degenerated. This causes non-monotonies in a mapping function. Although map for reducing this undesirable effect has already been proposed, it is defined theoretically and for standard genetic codes only. In this study, we derived a novel optimal criterion for reducing the influence of degeneration by utilizing a large dataset of real sequences with various genetic codes. As a result, we proposed a new robust global optimal map suitable for any genetic code as well as specialized optimal maps for particular genetic codes.

Amino acids; Bioinformatics; Codes (symbols); Computational methods; Large dataset; Mapping; Nucleotides; Computational task; Digital mapping; Digital representations; Mapping functions

Amino acids; Bioinformatics; Codes (symbols); Computational methods; Large dataset; Mapping; Nucleotides; Computational task; Digital mapping; Digital representations; Mapping functions

ŠKUTKOVÁ, H.; MADĚRÁNKOVÁ, D.; SEDLÁŘ, K.; JUGAS, R.; VÍTEK, M.

2019

01.02.2019

Elsevier

2001-0370

Computational and Structural Biotechnology Journal

17

1

Švédské království

406

414

9

http://www.sciencedirect.com/science/article/pii/S2001037018301557