Abstract
The study of genes is an important field of biology. A way to understand genetic composition is through finding regularly occurring nucleotide sequences, or motifs, in a DNA sequence. However, finding these motifs is difficult and is shown to be NP-complete. In this paper, we use a variant of P systems called Evolution-Communication P systems with Energy using string objects to solve the Motif Finding Problem in O(lt)-time where l is the length of the motif and t is the number of DNA sequences given.
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- 1.
In [5], the formal definition of \(\varPi _1\) has an initial membrane structure containing two membranes, i.e. \(\mu = [_1[_2]_2]_1\). However, it is apparent that even when removing membrane 2 and relocating the initial content of membrane 2, i.e. \(\beta _1\), and the rules of region 2 in the skin region, the algorithm still works almost the same. The only difference is the resources used.
- 2.
This is an entirely new subsystem compared to the subsystem \(\varPi _3\) in [5]. In [5], we were only able to solve for the restricted version of MFP because it can only find the motif if it has a unique maximum score. Otherwise, the system will just output an indication that the maximum score is not unique and therefore, won’t solve the problem.
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Acknowledgements
R. Juayong would like to thank the DOST-ERDT Scholarship Program and the DOST-PCIEERD for the HRIDD HRDP grant I-15-0715-2. N. Hernandez is supported by the Vea Family Technology for All Centennial professorial chair and the DOST-PCIEERD HRIDD HRDP grant I-15-1006-19. F. Cabarle is grateful for the support of the HRIDD HRDP grant I-15-0626-06 of the DOST PCIEERD, Philippines, a Faculty Incentive and Research Award (2015–2016) from the College of Engineering, UP Diliman, the PhDIA Project No. 161606 from the UP Diliman, OVCRD, and an RLC grant 20162017 also from OVCRD. H. Adorna is supported by the following, all from UP Diliman: Semirara Mining Corp. professorial chair, the Gawad Tsanselor Award grant 2015–2016 and an OVCRD RLC grant 2014–2015.
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Gapuz, K.B., Mendoza, E.D., Juayong, R.A.B., Hernandez, N.H.S., Cabarle, F.G.C., Adorna, H.N. (2017). Solution to Motif Finding Problem in Membranes. In: Leporati, A., Rozenberg, G., Salomaa, A., Zandron, C. (eds) Membrane Computing. CMC 2016. Lecture Notes in Computer Science(), vol 10105. Springer, Cham. https://doi.org/10.1007/978-3-319-54072-6_13
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