Publication detail

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

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

Original Title

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

English Title

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

Type

journal article in Scopus

Language

en

Original Abstract

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.

English abstract

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.

Keywords

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

Released

01.02.2019

Publisher

Elsevier

Pages from

406

Pages to

414

Pages count

9

URL

BibTex


@article{BUT156640,
  author="Helena {Škutková} and Denisa {Maděránková} and Karel {Sedlář} and Robin {Jugas} and Martin {Vítek}",
  title="A degeneration-reducing criterion for optimal digital mapping of genetic codes",
  annote="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.",
  address="Elsevier",
  chapter="156640",
  doi="10.1016/j.csbj.2019.03.007",
  howpublished="online",
  institution="Elsevier",
  number="1",
  volume="17",
  year="2019",
  month="february",
  pages="406--414",
  publisher="Elsevier",
  type="journal article in Scopus"
}