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Dc-coffee: A Novel Multiple Nucleic Acid Sequence Alignment Program Integrating the Divide-and-Conquer Strategy with the T-coffee Method.

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Title: Dc-coffee: A Novel Multiple Nucleic Acid Sequence Alignment Program Integrating the Divide-and-Conquer Strategy with the T-coffee Method.
Authors: E. L., Abdelhakim1 abdelhakim.elfatmi@uit.ac.ma, Ali, My2 ali.bekri@gmail.com
Source: IAENG International Journal of Computer Science. May2026, Vol. 53 Issue 5, p1823-1831. 9p.
Subjects: Sequence alignment, Nucleotide sequence, Optimization algorithms, Comparative genomics
Abstract: Nucleic acid sequence alignment is a fundamental task in molecular biology, playing a crucial role in the identification of functional domains, the analysis of evolutionary relationships, and the development of biotechnological and pharmaceutical applications. In comparative genomics, it enables the investigation of genome organization and evolutionary patterns, while in clinical research it supports the detection of pathogenic genetic variants and the understanding of gene regulation mechanisms. This study introduces a novel multiple nucleic acid sequence alignment method that combines a divide-and-conquer strategy with the T-coffee framework. The proposed approach improves both alignment accuracy and computational efficiency. The divide-and-conquer paradigm optimizes resource utilization and facilitates parallel execution, whereas the integration of T-coffee leverages information from multiple sources to produce reliable and accurate alignments. The performance of the proposed method is evaluated using the BraliBase II benchmark and the Rfam database, and compared with existing alignment tools. Experimental results demonstrate that the proposed approach provides an efficient and robust solution for multiple sequence alignment, enabling more effective analysis of complex nucleic acid sequence relationships. [ABSTRACT FROM AUTHOR]
Copyright of IAENG International Journal of Computer Science is the property of International Association of Engineers (IAENG) and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Dc-coffee: A Novel Multiple Nucleic Acid Sequence Alignment Program Integrating the Divide-and-Conquer Strategy with the T-coffee Method.
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  Data: <searchLink fieldCode="AR" term="%22E%2E+L%2E%2C+Abdelhakim%22">E. L., Abdelhakim</searchLink><relatesTo>1</relatesTo><i> abdelhakim.elfatmi@uit.ac.ma</i><br /><searchLink fieldCode="AR" term="%22Ali%2C+My%22">Ali, My</searchLink><relatesTo>2</relatesTo><i> ali.bekri@gmail.com</i>
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  Data: <searchLink fieldCode="JN" term="%22IAENG+International+Journal+of+Computer+Science%22">IAENG International Journal of Computer Science</searchLink>. May2026, Vol. 53 Issue 5, p1823-1831. 9p.
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  Data: <searchLink fieldCode="DE" term="%22Sequence+alignment%22">Sequence alignment</searchLink><br /><searchLink fieldCode="DE" term="%22Nucleotide+sequence%22">Nucleotide sequence</searchLink><br /><searchLink fieldCode="DE" term="%22Optimization+algorithms%22">Optimization algorithms</searchLink><br /><searchLink fieldCode="DE" term="%22Comparative+genomics%22">Comparative genomics</searchLink>
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  Label: Abstract
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  Data: Nucleic acid sequence alignment is a fundamental task in molecular biology, playing a crucial role in the identification of functional domains, the analysis of evolutionary relationships, and the development of biotechnological and pharmaceutical applications. In comparative genomics, it enables the investigation of genome organization and evolutionary patterns, while in clinical research it supports the detection of pathogenic genetic variants and the understanding of gene regulation mechanisms. This study introduces a novel multiple nucleic acid sequence alignment method that combines a divide-and-conquer strategy with the T-coffee framework. The proposed approach improves both alignment accuracy and computational efficiency. The divide-and-conquer paradigm optimizes resource utilization and facilitates parallel execution, whereas the integration of T-coffee leverages information from multiple sources to produce reliable and accurate alignments. The performance of the proposed method is evaluated using the BraliBase II benchmark and the Rfam database, and compared with existing alignment tools. Experimental results demonstrate that the proposed approach provides an efficient and robust solution for multiple sequence alignment, enabling more effective analysis of complex nucleic acid sequence relationships. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of IAENG International Journal of Computer Science is the property of International Association of Engineers (IAENG) and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Text: English
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        StartPage: 1823
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      – SubjectFull: Sequence alignment
        Type: general
      – SubjectFull: Nucleotide sequence
        Type: general
      – SubjectFull: Optimization algorithms
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      – SubjectFull: Comparative genomics
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      – TitleFull: Dc-coffee: A Novel Multiple Nucleic Acid Sequence Alignment Program Integrating the Divide-and-Conquer Strategy with the T-coffee Method.
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              Text: May2026
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