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Journal : Sinkron : Jurnal dan Penelitian Teknik Informatika

Comparative Analysis of DNA Sequence Alignment Algorithms in SARS-CoV-2 Edi, Edi; Robet, Robet; Harahap, Nurhayati
Sinkron : jurnal dan penelitian teknik informatika Vol. 9 No. 4 (2025): Articles Research October 2025
Publisher : Politeknik Ganesha Medan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33395/sinkron.v9i4.15323

Abstract

Sequence alignment is fundamental in bioinformatics, with Smith-Waterman (local) and Needleman-Wunsch (global) algorithms widely applied. However, comparative analyses on highly similar viral genomes such as SARS-CoV-2 remain scarce. This study systematically evaluated both algorithms using the first 5,000 nucleotides of two SARS-CoV-2 genomes (29,903 and 29,684 nt) under four parameter configurations: standard, low gap penalty, high gap penalty, and high match reward. Performance was assessed through alignment score, sequence identity, gap distribution, execution time, and parameter sensitivity. Both algorithms produced identical sequence identity (97.80%), with 4,943 matches out of 5,054 positions. Smith-Waterman consistently yielded higher alignment scores (12.6-112 points advantage), while Needleman-Wunsch was substantially faster (0.7752 vs 3.9014 s), showing 5.03 times greater computational efficiency. These findings indicate that both methods are reliable for highly similar viral sequences, with a trade-off between scoring precision and computational speed. This study provides the first parameter-sensitive comparison for full SARS-CoV02 genomes, emphasizing how parameter tuning can influence performance outcomes. A key limitation is that the analysis was restricted to the first 5,000 nucleotides, which may not capture variability across the complete genome.
Co-Authors Abdul Aziz Rusman Ahmad Laut Hasibuan Alfi, Mairanda Amrin Saragih Arifianti, Sari Maharani Asnawi Asnawi Aziza, Riska Bambang Riyanto Batubara, Irpan Apandi Batubara, Khoirunnisa'a Bincar Nasution Dwi Widayati, Dwi Dwita Putri, Riri edi edi Emma Marsella Eryadi, Alifia Fatahilla, Lou Ginting, Vivi Erinsyah br Guniesti, Veryani Gurning, Elisabet Intan Berlian Gustianingsih Gustianingsih, Gustianingsih Harianja, Anjelina Septiana Hasibuan, Purnama Hasibuan, Purnama Hidayat Husnul Khatima, Husnul Hutagalung, Renaldi Ida Basaria Indahsari, Wahyu Karina Ujung, Siti Khoiriyah Kesuma, Dani Khairani, Devia Astry Kharani, Suci Kudadiri, Amhar Lubis, Haris Sutan Lubis, Nabila Lubis, Nazriani Marsella, Emma Melati, Putri Indah Munthe, Indriyani Rehulina Br Nabila, Dara Nabila Nainggolan, Elisabet Natalia Hilleri Nasution, Silpiah Jahra Nauli, Rahel Chelsea Noperiyanti, Yola Novita Sari Novita Wulandari Novita, Winda Duwi Nur Ainun Nur Qulby, Tara Latifah Nurussakinah Daulay Panisa, Panisa Purba, Yutri Fahira Putri, Apriliani Alicia Putri, Salsabila Rachman, Syahvira Ramadani, Salwa Ritonga, Parlaungan Robet Robet Rokan, Mustafa Khamal S, Marsel Saulina Saiful Akhyar Lubis Saliyanti Salliyanti, Salliyanti Saragih, Sepen Wila Sibagariang, Lastarida Sijabat, Siska Geofani Simamora, Jose Maduma Sinaga, Herlin Nadia Singarimbun, Maya Sabet Ulina Siregar, Hazanasri Putri Rahmi Siti Hajar Sitohang, Desi Hotmaida Soemitra , Andri Sulaiman Sitompul, Gandi Surbakti, Bremakila Rangga Susilo, Hariadi Tamba, Ambrosia Tantawi, Isma TRIANA, ADE Trisnadiyah, Ahyunda Tumanggor, Winny R.E. Wahyuni, Ema Wantania, Pingkan Agnes Soraya Wariyati, Wariyati yanti, asmima Yulia Febrianti Yusoff , Murni Zuhdi, Muhammad Farhan