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Efficient Multiple Sequences Alignment Algorithm Generation via Components Assembly Under PAR Framework

As a key algorithm in bioinformatics, sequence alignment algorithm is widely used in sequence similarity analysis and genome sequence database search. Existing research focuses mainly on the specific steps of the algorithm or is for specific problems, lack of high-level abstract domain algorithm fra...

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Autores principales: Shi, Haipeng, Shi, Haihe, Xu, Shenghua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7890700/
https://www.ncbi.nlm.nih.gov/pubmed/33613626
http://dx.doi.org/10.3389/fgene.2020.628175
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author Shi, Haipeng
Shi, Haihe
Xu, Shenghua
author_facet Shi, Haipeng
Shi, Haihe
Xu, Shenghua
author_sort Shi, Haipeng
collection PubMed
description As a key algorithm in bioinformatics, sequence alignment algorithm is widely used in sequence similarity analysis and genome sequence database search. Existing research focuses mainly on the specific steps of the algorithm or is for specific problems, lack of high-level abstract domain algorithm framework. Multiple sequence alignment algorithms are more complex, redundant, and difficult to understand, and it is not easy for users to select the appropriate algorithm; some computing errors may occur. Based on our constructed pairwise sequence alignment algorithm component library and the convenient software platform PAR, a few expansion domain components are developed for multiple sequence alignment application domain, and specific multiple sequence alignment algorithm can be designed, and its corresponding program, i.e., C++/Java/Python program, can be generated efficiently and thus enables the improvement of the development efficiency of complex algorithms, as well as accuracy of sequence alignment calculation. A star alignment algorithm is designed and generated to demonstrate the development process.
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spelling pubmed-78907002021-02-19 Efficient Multiple Sequences Alignment Algorithm Generation via Components Assembly Under PAR Framework Shi, Haipeng Shi, Haihe Xu, Shenghua Front Genet Genetics As a key algorithm in bioinformatics, sequence alignment algorithm is widely used in sequence similarity analysis and genome sequence database search. Existing research focuses mainly on the specific steps of the algorithm or is for specific problems, lack of high-level abstract domain algorithm framework. Multiple sequence alignment algorithms are more complex, redundant, and difficult to understand, and it is not easy for users to select the appropriate algorithm; some computing errors may occur. Based on our constructed pairwise sequence alignment algorithm component library and the convenient software platform PAR, a few expansion domain components are developed for multiple sequence alignment application domain, and specific multiple sequence alignment algorithm can be designed, and its corresponding program, i.e., C++/Java/Python program, can be generated efficiently and thus enables the improvement of the development efficiency of complex algorithms, as well as accuracy of sequence alignment calculation. A star alignment algorithm is designed and generated to demonstrate the development process. Frontiers Media S.A. 2021-02-04 /pmc/articles/PMC7890700/ /pubmed/33613626 http://dx.doi.org/10.3389/fgene.2020.628175 Text en Copyright © 2021 Shi, Shi and Xu. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Shi, Haipeng
Shi, Haihe
Xu, Shenghua
Efficient Multiple Sequences Alignment Algorithm Generation via Components Assembly Under PAR Framework
title Efficient Multiple Sequences Alignment Algorithm Generation via Components Assembly Under PAR Framework
title_full Efficient Multiple Sequences Alignment Algorithm Generation via Components Assembly Under PAR Framework
title_fullStr Efficient Multiple Sequences Alignment Algorithm Generation via Components Assembly Under PAR Framework
title_full_unstemmed Efficient Multiple Sequences Alignment Algorithm Generation via Components Assembly Under PAR Framework
title_short Efficient Multiple Sequences Alignment Algorithm Generation via Components Assembly Under PAR Framework
title_sort efficient multiple sequences alignment algorithm generation via components assembly under par framework
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7890700/
https://www.ncbi.nlm.nih.gov/pubmed/33613626
http://dx.doi.org/10.3389/fgene.2020.628175
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