دورية أكاديمية
Correctness by Construction for Pairwise Sequence Alignment Algorithm in Bio-Sequence
| العنوان: | Correctness by Construction for Pairwise Sequence Alignment Algorithm in Bio-Sequence |
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| المؤلفون: | Haihe Shi, Sunwen Lan, Riming Liu, Haipeng Shi |
| المصدر: | Tehnički Vjesnik, Vol 30, Iss 3, Pp 742-749 (2023) |
| بيانات النشر: | Faculty of Mechanical Engineering in Slavonski Brod, Faculty of Electrical Engineering in Osijek, Faculty of Civil Engineering in Osijek, 2023. |
| سنة النشر: | 2023 |
| المجموعة: | LCC:Engineering (General). Civil engineering (General) |
| مصطلحات موضوعية: | automatic verification, correctness by construction, pairwise sequence alignment, PAR method, Engineering (General). Civil engineering (General), TA1-2040 |
| الوصف: | Pairwise sequence alignment is a classical problem in bioinformatics, aiming at finding the similarity between two sequences, which is important for discovering functional, structural and evolutionary information in biological sequences. More algorithms have been developed for the sequence alignment problem. There is no formal development process for the existing pairwise sequence algorithms and leads to the low trustworthiness of those algorithms. In addition, the application of formal methods in the field of bioinformatics algorithm development is rarely seen. In this paper, we use a formal method PAR to construct a pairwise sequence algorithm, analyze the essence of the pairwise sequence alignment problem, construct the Apla algorithm program by stepwise refinement, and further verify its correctness. Finally a highly reliable and executable pairwise sequence alignment algorithm program is generated from Apla program via PAR platform. The formal construction process ensures the reliability of algorithm, and also demonstrates the algorithm design idea clearly, which makes the originally difficult algorithm design process easier. The successful practice of this method on the pairwise sequence alignment problem in biological sequence analysis can provide a reference for the construction of highly reliable algorithms in complex bioinformatics from both methodological and practical aspects. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1330-3651 1848-6339 |
| Relation: | https://hrcak.srce.hr/file/433787; https://doaj.org/toc/1330-3651; https://doaj.org/toc/1848-6339 |
| DOI: | 10.17559/TV-20221025164232 |
| URL الوصول: | https://doaj.org/article/87ee45c2064845d6bd1e643abfa30e6d |
| رقم الأكسشن: | edsdoj.87ee45c2064845d6bd1e643abfa30e6d |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 13303651 18486339 |
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| DOI: | 10.17559/TV-20221025164232 |