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The problems of biological sequence analysis have great theoretical and practical value in modern bioinformatics. Numerous solving algorithms are used for these problems, and complex similarities and differences exist among these algorithms for the same problem, causing difficulty for researchers to select the appropriate one. To address this situation, combined with the formal partition-and-recur method, component technology, domain engineering, and generic programming, the paper presents a method for the development of a family of biological sequence analysis algorithms. It designs highly trustworthy reusable domain algorithm components and further assembles them to generate specifific biological sequence analysis algorithms. The experiment of the development of a dynamic programming based LCS algorithm family shows the proposed method enables the improvement of the reliability, understandability, and development efficiency of particular algorithms.
The problems of biological sequence analysis have great theoretical and practical value in modern bioinformatics. Numerous solving algorithms are used for these problems, and complex similarities and differences exist among these algorithms for the same problem, causing difficulty for researchers to select the appropriate one. To address this situation, combined with the formal partition-and-recur method, component technology, domain engineering, and generic programming, the paper presents a method for the development of a family of biological sequence analysis algorithms. It designs highly trustworthy reusable domain algorithm components and further assembles them to generate specifific biological sequence analysis algorithms. The experiment of the development of a dynamic programming based LCS algorithm family shows the proposed method enables the improvement of the reliability, understandability, and development efficiency of particular algorithms.
This work was supported by the National Natural Science Foundation of China (No. 62062039) and Natural Science Foundation of Jiangxi Province (Nos. 20202BAB202024 and 20212BAB202017).
The articles published in this open access journal are distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/).