Minimal state automata for detecting a β globin gene mutation

• Autorzy: Ferdania Devi Fitri , Irawati , Garminia Hanni , Akhmaloka , Rachmansyah Kemal Aziez

Identyfikatory

DOI

10.34768/amcs-2021-0023

• Języki publikacji: EN

Abstrakty

EN

Beta-thalassemia is an autosomal recessive blood disorder characterized by abnormalities in the synthesis of β globin. Together with α globin, it is a subunit of globin protein, called hemoglobin, located inside our red blood cells to deliver oxygen from the lungs to all of the tissues throughout our body. Thereby, individuals with β-thalassemia will often feel limp due to a lack of oxygen dissolved in their blood. In this paper, a finite state automaton to detect and classify β globin gene mutations using its DNA sequence is constructed. Finite state automata have a close connection to an algebraic structure, that is, a monoid. Together with the theory of the syntactic monoid, we present a methodology to minimize the number of the internal states of an automaton to have minimal state automata. Therefore, a minimal state automaton can be constructed to detect β globin gene mutation causing the β-thalassemia disease. We have developed a MATLAB program to conduct the appropriate simulations.

Słowa kluczowe

EN

minimal state automata; syntactic monoid; β-thalassemia; biological sequences

PL

automat stanu minimalnego; monoid syntaktyczny; sekwencja biologiczna

• Wydawca: Oficyna Wydawnicza Uniwersytetu Zielonogórskiego
• Czasopismo: International Journal of Applied Mathematics and Computer Science
• Rocznik: 2021
• Tom: Vol. 31, no. 2
• Strony: 337--351
• Opis fizyczny: Bibliogr. 19 poz., rys., tab.

Twórcy

autor

Ferdania Devi Fitri

• Algebra Research Group, Bandung Institute of Technology, Jl. Ganesha No.10, Jawa Barat, Bandung, Indonesia

autor

Irawati

• Algebra Research Group, Bandung Institute of Technology, Jl. Ganesha No.10, Jawa Barat, Bandung, Indonesia

autor

Garminia Hanni

• Algebra Research Group, Bandung Institute of Technology, Jl. Ganesha No.10, Jawa Barat, Bandung, Indonesia

autor

Akhmaloka

• Biochemistry Research Group, Bandung Institute of Technology, Jl. Ganesha No.10, Jawa Barat, Bandung, Indonesia

autor

Rachmansyah Kemal Aziez

• Algebra Research Group, Bandung Institute of Technology, Jl. Ganesha No.10, Jawa Barat, Bandung, Indonesia

Bibliografia

• [1] Galanello, R. and Origa, R. (2010). Beta thalassemia, Orphanet Journal of Rare Diseases 5(11): 1–15, DOI: 10.1186/1750-1172-5-11.
• [2] Handayani, N.S.N. and Onggo, A.T. (2014). Identifikasi mutasi gen β-globin ekson 1 pada pembawa thalassemia, Biogenesis Jurnal Ilmiah Biologi 2(1): 63–69.
• [3] Hetzl, S. (2017). Automata and formal languages, Technical report, Vienna University of Technology, Vienna.
• [4] Howie, J.M. (1976). An Introduction to Semigroup Theory, Academic Press Inc., New York.
• [5] Husna, N., Sanka, I., Arif, A.A., Putri, C., Leonard, E., and Nur Handayani, N.S. (2017). Prevalence and distribution of thalassemia trait screening, Journal of Medical Science 49(3): 106–113, DOI: 10.19106/JMedSci004903201702.
• [6] Klima, O. and Polak, L. (2016). Syntactic structures of regular languages, Theoretical Computer Science 800: 125–141, DOI: 10.1016/j.tcs.2019.10.020.
• [7] Lie-Injo, L., Cai, S., Wahidijat, I., Moeslichan, S., Lim, M., Evangelista, L., Doherty, M. and Kan, Y. (1989). Beta-thalassemia mutations in Indonesia and their linkage to beta-haplotypes, American Journal of Human Genetics 45(6): 971–975.
• [8] Mazumdar, D. and Raha, S. (2008). Finite state machine for mutation, Advanced Modeling and Optimization 10(2): 241–265.
• [9] Mehdi, M. and Khan, A. (2016). DNA pattern analysis using Fa, Mealy, and Moore machines, International Journal of Computer Science and Information Security 14(8): 235–243.
• [10] Pal, J., Mazumdar, D. and Raha, S. (2016). An algebra for biological sequences, International Journal for Computational Biology 5(2): 28–40.
• [11] Papiez, A., Badie C. and Polanska, J. (2019). Machine learning techniques combined with dose profiles indicate radiation response biomarkers, International Journal of Applied Mathematics and Computer Science 29(1): 169–178, DOI: 10.2478/amcs-2019-0013.
• [12] Pin, J.E. (2019). Mathematical foundations of automata, Technical report, Paris Diderot University, Paris.
• [13] Planting, A. (2013). From Automata to Monoids and Back Again, PhD thesis, Radboud University Nijmegen, Nijmegen.
• [14] Reddy, P.S. and Dawud, M. (2015). Application of semigroup, Global Journal of Science Frontier Research 15(3): 16–26.
• [15] Searls, D.B. and Murphy, K.P. (1995). Automata theoretic models of mutation and alignment, Proceedings of the International Conference on Intelligent Systems in Molecular Biology, Cambridge, UK, pp. 341–349.
• [16] Straubing, H. and Weil, P. (2012). An introduction to finite automata and their connection to logic, in D. D’Souza and P. Shankar (Eds), Modern Applications of Automata Theory, World Scientific, Singapore, pp. 3–43.
• [17] Sunthornwat, R., Moore, E.J. and Temtanapat, Y. (2011). Detecting and classifying mutations in genetic code with an application to beta-thalassemia, Science Asia 37: 51–61, DOI: 10.2306/scienceasia1513-1874.2011.37.051.
• [18] Wahidayat, P.A., Sastroasmoro, S., Fucharoen, S., Setianingsih, I. and Putriasih, S.A. (2018). Applicability of a clinical scoring criteria for disease severity of β-thalassemia/hemoglobin E in Indonesia, Medical Journal of Indonesia 27(1): 26–32, DOI: 10.13181/mji.v27i1.1779.
• [19] Zok, T., Badura, J., Swat, S., Figurski, K., Popenda, M. and Antczak, M. (2020). New models and algorithms for RNA pseudoknot order assignment, International Journal of Applied Mathematics and Computer Science 30(2): 315–324, DOI: 10.34768/amcs-2020-0024.

Uwagi

Opracowanie rekordu ze środków MNiSW, umowa Nr 461252 w ramach programu "Społeczna odpowiedzialność nauki" - moduł: Popularyzacja nauki i promocja sportu (2021).