A degeneration-reducing criterion for optimal digital mapping of genetic codes
| Autor: | Robin Jugas, Denisa Maderankova, Martin Vitek, Karel Sedlar, Helena Skutkova |
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| Rok vydání: | 2019 |
| Předmět: |
0303 health sciences
Mathematical problem Digital mapping Computer science lcsh:Biotechnology String (computer science) Biophysics Scientific field Function (mathematics) Genetic code Biochemistry Computer Science Applications Global optimal 03 medical and health sciences ComputingMethodologies_PATTERNRECOGNITION 0302 clinical medicine Structural Biology lcsh:TP248.13-248.65 030220 oncology & carcinogenesis Genetics Digital signal Short Survey Algorithm 030304 developmental biology Biotechnology |
| Zdroj: | Computational and Structural Biotechnology Journal Computational and Structural Biotechnology Journal, Vol 17, Iss, Pp 406-414 (2019) |
| ISSN: | 2001-0370 |
| DOI: | 10.1016/j.csbj.2019.03.007 |
| Popis: | 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. Graphical Abstract Unlabelled Image Highlights • Optimization of 1D numerical representation for DNA to protein translation. • Reducing genetic code degeneracy in numerical representation of DNA sequences. • More robust numerical conversion used for genomic-proteomic analysis. |
| Databáze: | OpenAIRE |
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