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Construction of Cyclic Codes over \({\mathbb {Z}}_{20}\) for Identifying Proteins

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Applied Computer Sciences in Engineering (WEA 2019)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 1052))

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Abstract

For biology, engineering and biotechnology, among others sciences related with the subject, it is essential to understand the role of proteins in the genetic information transmission process in order to conclude about evolution, changes, and connection between species. In recent work, protein synthesis process has been compared with a digital transmission system and, thus, algorithms which allow identifying biological sequences as code-words of BCH codes were developed to verify the validity of this model. Algorithms in literature are limited in respect to the length of the biological sequence, which creates restrictions when establishing taxonomic and phylogenetic inferences of living beings. In this work, we extend the number of sequences that can be analyzed by designing an algorithm that identifies, using cycling codes, biological sequences with odd length and, thus, it makes possible to find a relation between mathematical properties of cycling codes with biological properties (taxonomy and phylogeny).

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References

  1. Pérez, E.M., Mandado, E., Mandado, Y.: Sistemas electrónicos digitales. Marcombo (2007)

    Google Scholar 

  2. Battail, G.: Information theory and error-correcting codes in genetics and biological evolution. In: Barbieri, M. (ed.) Introduction to Biosemiotics, pp. 299–345. Springer, Dordrecht (2008). https://doi.org/10.1007/1-4020-4814-9_13

    Chapter  Google Scholar 

  3. Gierasch, L.M., Horwich, A., Slingsby, C., Wickner, S., Agard, D.: Structure and Action of Molecular Chaperones: Machines that Assist Protein Folding in the Cell. WorldScientific (2016)

    Google Scholar 

  4. Calabrese, R.L.: Channeling the central dogma. Neuron 82(4), 725–727 (2014)

    Article  Google Scholar 

  5. Duarte-González, M., Echeverri, O., Guevara, J., Palazzo Jr., R.: Cyclic concatenated genetic encoder: a mathematical proposal for biological inferences. Biosystems 163, 47–58 (2018)

    Article  Google Scholar 

  6. Barbieri, M.: Code biology-a new science of life. Biosemiotics 5(3), 411–437 (2012)

    Article  Google Scholar 

  7. Nelson, D.L., Lehninger, A.L., Cox, M.M.: Lehninger Principles of Biochemistry. Macmillan, London (2008)

    Google Scholar 

  8. Liu, Y., et al.: Impact of alternative splicing on the human proteome. Cell Rep. 20(5), 1229–1241 (2017)

    Article  Google Scholar 

  9. Faria, L., Rocha, A., Kleinschmidt, J., Palazzo, R., Silva-Filho, M.: DNA sequences generated by BCH codes over GF (4). Electron. Lett. 46(3), 203–204 (2010)

    Article  Google Scholar 

  10. Rocha, A.S.L., Faria, L.C.B., Kleinschmidt, J.H., Palazzo, R., Silva-Filho, M.C.: DNA sequences generated by Z4-linear codes. In: 2010 IEEE International Symposium on Information Theory Proceedings (ISIT), pp. 1320–1324. IEEE (2010)

    Google Scholar 

  11. Duarte Gonzalez, M.E.: Modelagem da síntese de proteínas e sua estrutura organizacional através de códigos corretores de erros. [recurso eletrônico]. Ph.D. dissertation (2017)

    Google Scholar 

  12. Brandão, M.M., Spoladore, L., Faria, L.C., Rocha, A.S., Silva-Filho, M.C., Palazzo, R.: Ancient DNA sequence revealed by error-correcting codes. Sci. Rep. 5, 12051 (2015)

    Article  Google Scholar 

  13. Faria, L., Rocha, A., Palazzo Jr., R.: Transmission of intra-cellular genetic information: a system proposal. J. Theor. Biol. 358, 208–231 (2014)

    Article  MathSciNet  Google Scholar 

  14. Taylor, W.R.: The classification of amino acid conservation. J. Theor. Biol. 119(2), 205–218 (1986)

    Article  MathSciNet  Google Scholar 

  15. Guenda, K., Gulliver, T.A.: Construction of cyclic codes over \({\mathbb{F}}_{2}+ u{\mathbb{F}}_{2}\) for DNA computing. Appl. Algebra Eng. Commun. Comput. 24(6), 445–459 (2013)

    Google Scholar 

  16. Blake, I.F.: Codes over certain rings. Inf. Control, 20(4), 396–404 (1972). http://www.sciencedirect.com/science/article/pii/S0019995872902239

    Article  MathSciNet  Google Scholar 

  17. Dougherty, S.T., Harada, M., Solé, P.: Self-dual codes over rings and the Chinese remainder theorem. Hokkaido Math. J. 28(2), 253–283 (1999). https://doi.org/10.14492/hokmj/1351001213

    Article  MathSciNet  Google Scholar 

  18. Faria, L.C., et al.: Is a genome a codeword of an error-correcting code? PloS One 7(5), e36644 (2012)

    Article  Google Scholar 

  19. Palazzo Jr., R.: Álgebra e Códigos de Bloco. Universidade Estadual de Campinas (UNICAMP) (2013)

    Google Scholar 

  20. Huffman, W.C., Pless, V.: Fundamentals of Error-Correcting Codes. Cambridge University Press, Cambridge (2010)

    MATH  Google Scholar 

  21. Peterson, W.W., Peterson, W., Weldon, E., Weldon, E.: Error-Correcting Codes. MIT Press, Cambridge (1972)

    MATH  Google Scholar 

  22. Geer, L.Y., et al.: The NCBI BioSystems database. Nucleic Acids Res. 38(Suppl. 1), D492–D496 (2009)

    MathSciNet  Google Scholar 

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Acknowledgment

Authors thank Universidad Antonio Nariño (project number: 2017224) and Pontificia Universidad Javeriana - Bogotá (project ID: 7830).

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Authors and Affiliations

  1. Faculty of Mechanical, Electronic and Biomedical Engineering, Antonio Nariño University, Bogotá, Colombia

    Valentina Galíndez Gómez & Mario Enrique Duarte González

Authors
  1. Valentina Galíndez Gómez
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  2. Mario Enrique Duarte González
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Corresponding author

Correspondence to Valentina Galíndez Gómez .

Editor information

Editors and Affiliations

  1. Department of Industrial Engineering, Universidad Distrital Francisco José de Caldas, Bogotá, Colombia

    Juan Carlos Figueroa-García

  2. Universidad Antonio Nariño, Bogotá, Colombia

    Mario Duarte-González

  3. Universidad Antonio Nariño, Bogotá, Colombia

    Sebastián Jaramillo-Isaza

  4. Universidad del Rosario, Bogotá, Colombia

    Alvaro David Orjuela-Cañon

  5. Corporación Unificada Nacional CUN, Bogotá, Colombia

    Yesid Díaz-Gutierrez

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Galíndez Gómez, V., Duarte González, M.E. (2019). Construction of Cyclic Codes over \({\mathbb {Z}}_{20}\) for Identifying Proteins. In: Figueroa-García, J., Duarte-González, M., Jaramillo-Isaza, S., Orjuela-Cañon, A., Díaz-Gutierrez, Y. (eds) Applied Computer Sciences in Engineering. WEA 2019. Communications in Computer and Information Science, vol 1052. Springer, Cham. https://doi.org/10.1007/978-3-030-31019-6_4

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  • DOI: https://doi.org/10.1007/978-3-030-31019-6_4

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-31018-9

  • Online ISBN: 978-3-030-31019-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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