Component-Based Design and Assembly of Heuristic Multiple Sequence Alignment Algorithms

In recent years, there has been an explosive increase in the amount of bioinformatics data produced, but data are not information. The purpose of bioinformatics research is to obtain information with biological significance from large amounts of data. Multiple sequence alignment is widely used in se...

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Vydané v:Frontiers in genetics Ročník 11; s. 105
Hlavní autori: Shi, Haihe, Zhang, Xuchu
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: Switzerland Frontiers Media S.A 27.02.2020
Predmet:
component interaction model
feature model
generative programming
Genetics
heuristic multiple sequence alignment algorithms
partition and recur platform
partition and recur platform
generative programming
feature model
component interaction model
heuristic multiple sequence alignment algorithms
ISSN:1664-8021, 1664-8021
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Shrnutí:In recent years, there has been an explosive increase in the amount of bioinformatics data produced, but data are not information. The purpose of bioinformatics research is to obtain information with biological significance from large amounts of data. Multiple sequence alignment is widely used in sequence homology detection, protein secondary and tertiary structure prediction, phylogenetic tree analysis, and other fields. Existing research mainly focuses on the specific steps of the algorithm or on specific problems, and there is a lack of high-level abstract domain algorithm frameworks. As a result, multiple sequence alignment algorithms are complex, redundant, and difficult to understand, and it is not easy for users to select the appropriate algorithm, which may lead to computing errors. Here, through in-depth study and analysis of the heuristic multiple sequence alignment algorithm (HMSAA) domain, a domain-feature model and an interactive model of HMSAA components have been established according to the generative programming method. With the support of the PAR (partition and recur) platform, the HMSAA algorithm component library is formalized and a specific alignment algorithm is assembled, thus improving the reliability of algorithm assembly. This work provides a valuable theoretical reference for the applications of other biological sequence analysis algorithms.
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This article was submitted to Bioinformatics and Computational Biology, a section of the journal Frontiers in Genetics
Edited by: Yanjie Wei, Shenzhen Institutes of Advanced Technology (CAS), China
Reviewed by: Pu-Feng Du, Tianjin University, China; Wang-Ren Qiu, Jingdezhen Ceramic Institute, China; Weiguo Liu, Shandong University, China
ISSN:1664-8021
1664-8021
DOI:10.3389/fgene.2020.00105