Loading [MathJax]/extensions/MathZoom.js
DNA Pattern Matching Algorithms within Sorghum bicolor Genome: A Comparative Study | IEEE Conference Publication | IEEE Xplore
Subscribe
ADVANCED SEARCH
Conferences >2024 7th International Confer...

DNA Pattern Matching Algorithms within Sorghum bicolor Genome: A Comparative Study

PDF
Dwika Lovitasari Yonia; Shintami Chusnul Hidayati; Riyanarto Sarno; Abdullah Faqih Septiyanto
All Authors

Abstract:

Sorghum bicolor, a vital cereal crop with significant roles in agriculture and biofuel production, presents a complex genome that poses substantial challenges for genetic...Show More

Metadata

Abstract:

Sorghum bicolor, a vital cereal crop with significant roles in agriculture and biofuel production, presents a complex genome that poses substantial challenges for genetic analysis and improvement. This study provides a comprehensive comparison of DNA pattern-matching algorithms applied to the Sorghum bicolor genome, focusing on the accuracy, efficiency, and effectiveness of each technique. The algorithms evaluated include the simple Brute Force method, the efficient BoyerMoore algorithm, the linear-time Knuth-Morris-Pratt (KMP) algorithm, the Enhanced First-Last Pattern Matching (EFLPM), and the Enhanced Processor-Aware Pattern Matching (EPAPM). Notably, the EFLPM and EPAPM algorithms excel at accommodating errors and mutations in DNA sequences, with EPAPM additionally leveraging parallel processing techniques to enhance performance. This comparative study highlights the crucial role of temporal complexity in selecting the most suitable DNA pattern-matching algorithm for genomic analysis.
Published in: 2024 7th International Conference on Informatics and Computational Sciences (ICICoS)
Date of Conference: 17-18 July 2024
Date Added to IEEE Xplore: 21 August 2024
ISBN Information:

ISSN Information:

DOI: 10.1109/ICICoS62600.2024.10636821
Conference Location: Semarang, Indonesia

Funding Agency:

References is not available for this document.
Contents

I. Introduction

In bioinformatics, deciphering the complexities of deoxyribonucleic acid (DNA) is crucial for understanding biological phenomena at the molecular level. DNA, the foundation of life, encodes the genetic instructions vital for the development and functioning of all living organisms. These instructions are stored within the sequences of nitrogenous bases, constituting the genetic blueprint for proteins and RNA sequences [1]. The structural integrity of DNA, characterized by its iconic double helix, provides it with the resilience to withstand mechanical forces. However, it remains prone to certain deformations, such as twisting and bending [2]. The intricate sequence of nucleotide bases in DNA, consisting of adenine (A), guanine (G), cytosine (C), and thymine (T), encases extensive biophysical information. A thorough understanding of DNA’s structure is critical for elucidating gene expression, DNA replication, and chromosome segregation during cell division [3].

Select All
1.
R. Termanini, "The amazing human dna system explained", pp. 17-37, 2020.
CrossRef Google Scholar
2.
M. Asmamaw and B. Zawdie, "Mechanism and applications of crispr/cas-9-mediated genome editing", Biologics: Targets Therapy, vol. 15, pp. 353-361, 2021.
Google Scholar
3.
T. M. Escobar, A. Loyola and D. Reinberg, "Parental nucleosome segregation and the inheritance of cellular identity", Nature Reviews Genetics, vol. 22, pp. 379-392, 2021.
CrossRef Google Scholar
4.
M. Najam, R. Rasool, H. Ahmad, U. Ashraf and A. Malik, "Pattern matching for dna sequencing data using multiple bloom filters", Biomed Res Int, vol. 2019, pp. 7074387, 2019.
CrossRef Google Scholar
5.
O. Ibrahim, B. Hamed and T. El-Hafeez, "A new fast technique for pattern matching in biological sequences", J Supercomput, vol. 79, pp. 367-388, 2023.
CrossRef Google Scholar
6.
F. B. Ashraf, "Mfea: An evolutionary approach for motif finding in dna sequences", Informatics in Medicine Unlocked, vol. 21, pp. 11, 2020.
CrossRef Google Scholar
7.
F. Cruz, J. Gomez-Garrido, M. Gut, T. S. Alioto, J. Pons, J. Alos, et al., "Chromosome-level assembly and annotation of the xyrichtys novacula (linnaeus 1758) genome", DNA Research, vol. 30, no. 5, 2023.
CrossRef Google Scholar
8.
Y.-H. Hsieh, S. C. Hidayati, W.-H. Cheng, M.-C. Hu and K.-L. Hua, "Who’s the best charades player? mining iconic movement of semantic concepts", Proc. Int. Conf. MultiMedia Modeling, pp. 231-241, 2014.
CrossRef Google Scholar
9.
Z.-M. Liu, Y.-Y. Chen, S. Hidayati, S.-C. Chien, F.-C. Chang and K.-L. Hua, "3d model retrieval based on deep autoencoder neural networks", Proc. Int. Conf. Signals and Systems, pp. 290-296, 2017.
View Article
Google Scholar
10.
E. Massip, S. C. Hidayati, W.-H. Cheng and K.-L. Hua, "Exploiting category-specific information for image popularity prediction in social media", Proc. IEEE Int. Conf. Multimedia Expo Workshops, pp. 45-46, 2018.
View Article
Google Scholar
11.
N. Sinkovics, "Pattern matching in qualitative analysis", The SAGE Handbook of Qualitative Business and Management Research Methods: Methods and Challenges, pp. 468484, May 2018.
CrossRef Google Scholar
12.
A. A. Karcioglu and H. Bulut, "The wm-q multiple exact string matching algorithm for dna sequences", Computers in Biology and Medicine, vol. 136, pp. 104656, 2021.
CrossRef Google Scholar
13.
Y. Kim, M. Imani, N. Moshiri and T. Rosing, "Geniehd: Efficient dna pattern matching accelerator using hyperdimensional computing", 2020 Design Automation & Test in Europe Conference & Exhibition (DATE), pp. 115-120, 2020.
View Article
Google Scholar
14.
P. Neamatollahi, M. Hadi and M. Naghibzadeh, "Efficient pattern matching algorithms for dna sequences", Proc. International Computer Conference Computer Society of Iran, 2020.
View Article
Google Scholar
15.
A. V. Aho, "Algorithms for finding patterns in strings", Handbook of Theoretical Computer Science Algorithms and Complexity., pp. 255-300, 1990.
CrossRef Google Scholar
16.
R. S. Boyer and J. S. Moore, "A fast string searching algorithm", Commun. ACM, vol. 20, no. 10, pp. 762-772, 1977.
CrossRef Google Scholar
17.
C. Wang, L. Gong, S. Lei et al., "Genseq+: A scalable high-performance accelerator for genome sequencing", IEEE/ACM Trans Comput Biol Bioinform, vol. 18, no. 4, pp. 1512-1523, 2021.
View Article
Google Scholar
18.
X. Wu, Y. Liu, H. Luo, L. Shang, C. Leng, Z. Liu, et al., "Genomic footprints of sorghum domestication and breeding selection for multiple end uses", Molecular Plant, vol. 15, no. 3, pp. 537-551, 2022.
CrossRef Google Scholar
19.
Y. Cheng, W. Deng, Y. Lu, S. Han, Y. Lv, G. Zeng, et al., "Establishment of sorghum btx623 immature embryos genetic transformation and regeneration system", Molecular Plant Breeding, vol. 11, no. 5, 2020.
CrossRef Google Scholar
20.
Q. lin XIAO, Z. LI, Y. yun WANG, X. bin HOU, X. mei WEI, X. ZHAO, et al., "Genome-wide identification expression and functional analysis of sugar transporters in sorghum (sorghum bicolor 1.)", Journal of Integrative Agriculture, vol. 21, no. 10, pp. 2848-2864, 2022.
CrossRef Google Scholar
21.
M. F. Aza, N. Suciati and S. C. Hidayati, "Performance study of facial expression recognition using convolutional neural network", Proc. Int. Conf. Science in Information Technology, pp. 121-126, 2020.
View Article
Google Scholar
22.
S. C. Hidayati, T. W. Goh, J.-S. G. Chan, C.-C. Hsu, J. See, L.-K. Wong, et al., "Dress with style: Learning style from joint deep embedding of clothing styles and body shapes", IEEE Transactions on Multimedia, vol. 23, pp. 365-377, 2021.
View Article
Google Scholar
23.
A. Widyadhana, S. C. Hidayati, D. A. Navastara and Y. Anistyasari, "ASF-LLRDA: locality-regularized linear regression discriminant analysis with approximately symmetrical face preprocessing for face recognition", Asia Pacific Signal and Information Processing Association Annual Summit and Conference, pp. 2031-2036, 2023.
View Article
Google Scholar
24.
J. Kim and C. Kim, "A beginner’s guide to assembling a draft genome and analyzing structural variants with long-read sequencing technologies", STAR Protocols, vol. 3, no. 3, pp. 101506, 2022.
CrossRef Google Scholar
25.
T.-H. Tsai, W.-C. Jhou, W.-H. Cheng, M.-C. Hu, I.-C. Shen, T. Lim, et al., "Photo sundial: Estimating the time of capture in consumer photos", Neurocomputing, vol. 177, pp. 529-542, 2016.
CrossRef Google Scholar
26.
G. Marzani, N. Suciati and S. C. Hidayati, "Morphological preprocessing for low-resolution face recognition using common space", Proc. Int. Conf. ICT for Smart Society, pp. 1-5, 2021.
View Article
Google Scholar
27.
P. B. Abhale, "Handwritten english alphabet recognition", International Journal for Research in Applied Science and Engineering Technology, 2021.
CrossRef Google Scholar
28.
C. Barutu, N. Abdi, T. Informatika, S. Pontianak and Kalimantan, "Brute force algorithm implementation of dictionary search", Jurnal Info Sains: Informatika dan Sains, 2020.
CrossRef Google Scholar
29.
Y. Riwanto, M. Nuruzzaman, S. Uyun and B. Sugiantoro, "Data search process optimization using brute force and genetic algorithm hybrid method", International Journal on Informatics for Development, 2023.
CrossRef Google Scholar
30.
B. Browning, X. Tian, Y. Zhou and S. Browning, "Fast two-stage phasing of large-scale sequence data", American journal of human genetics, 2021.
CrossRef Google Scholar
Contact IEEE to Subscribe
More Like This
DNA Sequencing Using Machine Learning Algorithms

2022 International Conference on Data Science, Agents & Artificial Intelligence (ICDSAAI)

Published: 2022

Enhancing Weather Forecasting Accuracy: Integrating Machine Learning Algorithms with Numerical Weather Prediction Models

2024 1st International Conference on Advances in Computing, Communication and Networking (ICAC2N)

Published: 2024

Show More

References

References is not available for this document.

IEEE Account

Purchase Details

Profile Information

Need Help?

A not-for-profit organization, IEEE is the world's largest technical professional organization dedicated to advancing technology for the benefit of humanity.
© Copyright 2025 IEEE - All rights reserved. Use of this web site signifies your agreement to the terms and conditions.