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Sequence Alignment : Methods, Models, Concepts, and Strategies

• Authors : Michael S. Rosenberg Ph. D.

Subjects: Sequence alignment (Bioinformatics); Bioinformatics; Computational biologySCIENCE / Life Sciences / Evolution

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ProtAlign-ARG: antibiotic resistance gene characterization integrating protein language models and alignment-based scoring.

• Authors : Ahmed, Shafayat¹ (AUTHOR); Emon, Muhit Islam¹ (AUTHOR); Moumi, Nazifa Ahmed¹ (AUTHOR)

• Source: Scientific Reports. 8/18/2025, Vol. 15 Issue 1, p1-13. 13p.

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DeepSEA: an alignment-free explainable approach to annotate antimicrobial resistance proteins.

• Authors : Borelli, Tiago Cabral^1,2,3 (AUTHOR); Paschoal, Alexandre Rossi^4,5 (AUTHOR); da Silva, Ricardo Roberto^1,2 (AUTHOR)

• Source: BMC Bioinformatics. 9/1/2025, Vol. 26 Issue 1, p1-18. 18p.

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Assessing opportunities of SYCL for biological sequence alignment on GPU-based systems

• Authors : Manuel Costanzo; Enzo Rucci; Carlos García ...

Subjects: Parallel computing; Programmer; 0301 basic medicine

• Source: The Journal of Supercomputing. 80:12599-12622

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Enhanced Genetic Method for Optimizing Multiple Sequence Alignment.

• Authors : Ibrahim, Mohammed K.¹ (AUTHOR) ; Yusof, Umi Kalsom¹ (AUTHOR); Eisa, Taiseer Abdalla Elfadil² (AUTHOR)

• Source: Mathematics (2227-7390). Nov2023, Vol. 11 Issue 22, p4578. 23p.

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X-Mapper: fast and accurate sequence alignment via gapped x-mers

• Authors : Jeffry M. Gaston; Eric J. Alm; An-Ni Zhang

Subjects: Bioinformatics; Sequence alignment algorithms; K-mer

• Source: Genome Biology, Vol 26, Iss 1, Pp 1-27 (2025)

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A multi-objective fuzzy model based on enhanced artificial fish Swarm for multiple RNA sequences alignment

• Authors : Medhat A. Tawfeek; Ibrahim Alrashdi; Madallah Alruwaili

Subjects: Fuzzy multi-objective optimization; RNA sequences alignment; Bioinformatics

• Source: Egyptian Informatics Journal, Vol 29, Iss , Pp 100627- (2025)

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Dotplotic: a lightweight visualization tool for BLAST + alignments and genomic annotations.

• Authors : Miyazawa, Hideyuki¹ (AUTHOR) ; Oda, Toshiyuki¹ (AUTHOR)

• Source: BMC Bioinformatics. 8/27/2025, Vol. 26 Issue 1, p1-12. 12p.

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Mathematical Modeling in Bioinformatics: Application of an Alignment-Free Method Combined with Principal Component Analysis.

• Authors : Bielińska-Wąż, Dorota¹ (AUTHOR) ; Wąż, Piotr² (AUTHOR); Błaczkowska, Agata¹ (AUTHOR)

• Source: Symmetry (20738994). Aug2024, Vol. 16 Issue 8, p967. 20p.

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GPU Performance of Alignment Step in Next Generation Sequencing Analysis.

• Authors : Akarkamçı, Hilal¹ ; Özdoğan, Gülistan Özdemir¹

• Source: Gazi Journal of Engineering Sciences (GJES) / Gazi Mühendislik Bilimleri Dergisi. agu2024, Vol. 10 Issue 2, p432-442. 11p.

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