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Embed-Search-Align: DNA Sequence Alignment using Transformer models

• Authors : Holur, Pavan; Enevoldsen, K C; Rajesh, Shreyas ...

• Source: Bioinformatics ; ISSN 1367-4811

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ReAlign-N: an integrated realignment approach for multiple nucleic acid sequence alignment, combining global and local realignments

• Authors : Zhai, Yixiao; Zhou, Tong; Wei, Yanming ...

• Source: NAR Genomics and Bioinformatics ; volume 6, issue 4 ; ISSN 2631-9268

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BIMSA: accelerating long sequence alignment using processing-in-memory

• Authors : Alonso-Marín, Alejandro; Fernandez, Ivan; Aguado-Puig, Quim ...

• Source: Bioinformatics ; volume 40, issue 11 ; ISSN 1367-4811

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FORAlign: accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on Four Russians approach with linear space complexity

• Authors : Wei, Yanming; Zhou, Tong; Zhai, Yixiao ...

• Source: Briefings in Bioinformatics ; volume 26, issue 1 ; ISSN 1467-5463 1477-4054

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BSAlign: A Library for Nucleotide Sequence Alignment

• Authors : Shao, Haojing; Ruan, Jue; Zhang, Zhang

• Source: Genomics, Proteomics & Bioinformatics ; volume 22, issue 2 ; ISSN 1672-0229 2210-3244

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Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction

• Authors : Wei-Mou Zheng; Qi Zhang; Shiwei Sun

Subjects: Statistics and Probability; Sequence; Multiple sequence alignment

• Source: Bioinformatics. 38:990-996

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MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences

• Authors : Chengze Shen; Tandy Warnow; Paul Zaharias

Subjects: 0106 biological sciences; Statistics and Probability; AcademicSubjects/SCI01060

• Source: Bioinformatics

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BetaAlign: a deep learning approach for multiple sequence alignment

• Authors : Dotan, Edo; Wygoda, Elya; Ecker, Noa ...

• Source: Bioinformatics ; volume 41, issue 1 ; ISSN 1367-4811

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Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels

• Authors : Iglhaut, Clara; Pečerska, Jūlija; Gil, Manuel ...

• Source: Molecular Biology and Evolution ; volume 41, issue 7 ; ISSN 0737-4038 1537-1719

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FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets

• Authors : Zhang, Pinglu; Liu, Huan; Wei, Yanming ...

• Source: Bioinformatics ; volume 40, issue 1 ; ISSN 1367-4803 1367-4811

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