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Generating Minimal Models of H1N1 NS1 Gene Sequences Using Alignment-Based and Alignment-Free Algorithms

التفاصيل البيبلوغرافية
العنوان: Generating Minimal Models of H1N1 NS1 Gene Sequences Using Alignment-Based and Alignment-Free Algorithms
المؤلفون: Meng Fang, Jiawei Xu, Nan Sun, Stephen S.-T. Yau
المصدر: Genes, Vol 14, Iss 1, p 186 (2023)
بيانات النشر: MDPI AG, 2023.
سنة النشر: 2023
المجموعة: LCC:Genetics
مصطلحات موضوعية: minimal model, longest common sequence, multiple sequence alignment, natural vector, virus tracing, Genetics, QH426-470
الوصف: For virus classification and tracing, one idea is to generate minimal models from the gene sequences of each virus group for comparative analysis within and between classes, as well as classification and tracing of new sequences. The starting point of defining a minimal model for a group of gene sequences is to find their longest common sequence (LCS), but this is a non-deterministic polynomial-time hard (NP-hard) problem. Therefore, we applied some heuristic approaches of finding LCS, as well as some of the newer methods of treating gene sequences, including multiple sequence alignment (MSA) and k-mer natural vector (NV) encoding. To evaluate our algorithms, a five-fold cross validation classification scheme on a dataset of H1N1 virus non-structural protein 1 (NS1) gene was analyzed. The results indicate that the MSA-based algorithm has the best performance measured by classification accuracy, while the NV-based algorithm exhibits advantages in the time complexity of generating minimal models.
نوع الوثيقة: article
وصف الملف: electronic resource
اللغة: English
تدمد: 14010186
2073-4425
Relation: https://www.mdpi.com/2073-4425/14/1/186; https://doaj.org/toc/2073-4425
DOI: 10.3390/genes14010186
URL الوصول: https://doaj.org/article/a27c043a2e5d40b0842b69b7427fd21d
رقم الأكسشن: edsdoj.27c043a2e5d40b0842b69b7427fd21d
قاعدة البيانات: Directory of Open Access Journals
الوصف
تدمد:14010186
20734425
DOI:10.3390/genes14010186