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WFAsic: A high-performance ASIC accelerator for DNA sequence alignment on a RISC-V SoC

• Authors : Haghi, Abbas; Álvarez Martí, Lluc; Fornt Mas, Jordi ...

Subjects: Àrees temàtiques de la UPC::Informàtica::Arquitectura de computadors; Genomics; Microprocessors -- Design and construction

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GMX: Instruction set extensions for fast, scalable, and efficient genome sequence alignment

• Authors : Doblas Font, Max; Lostes Cazorla, Oscar; Aguado Puig, Quim ...

Subjects: Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica; Genomics; Dynamic programming

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Parallelization of the Banded Needleman & Wunsch Algorithm on UPMEM PiM Architecture for Long DNA Sequence Alignment

• Authors : Mognol, Meven; Lavenier, Dominique; Legriel, Julien ...

Subjects: Theory of computation → Massively parallel algorithms Pattern matching • Hardware → Memory and dense storage Processing-in-Memory; long read Alignment; parallelismGotland; Sweden

• Source: ICPP 2024 - International Conference on Parallel Processing ; https://hal.science/hal-04739328 ; ICPP 2024 - International Conference on Parallel Processing, Aug 2024, Gotland, Sweden. pp.1-10

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FPGA-based protein sequence alignment : A review.

• Authors : Md. Isa, Mohd. Nazrin¹ ; Ku Muhsen, Ku Noor Dhaniah¹; Nurdin, Dayana Saiful¹

• Source: EPJ Web of Conferences. 2017, Vol. 162, p1-5. 5p. 9 Diagrams, 1 Chart.

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Self-Sequence Alignment - Implementation vs model.pptx

• Authors : Paul Gagniuc (1818325)

Subjects: Bioinformatics; Computational Biology; Self Sequence Alignment

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A CGM-Based Parallel Algorithm Using the Four-Russians Speedup for the 1-D Sequence Alignment Problem

• Authors : Lacmou Zeutouo, Jerry; Tessa Masse, Grace Colette; KAMGA YOUMBI, Franklin Ingrid ...

Subjects: parallel algorithm; CGM model; dynamic programmingThiès; Senegal

• Source: CARI 2020 - Colloque Africain pour la Recherche en Informatique et Mathématiques Appliquées ; https://hal.archives-ouvertes.fr/hal-02925791 ; CARI 2020 - Colloque Africain pour la Recherche en

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TALCO: Tiling Genome Sequence Alignment using Convergence of Traceback Pointers

• Authors : Walia, Sumit; Turakhia, Yatish;

• Source: HPCA, IEEE International Symposium on High-Performance Computer Architecture

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Niema Moshiri: Massively scalable reference-guided Multiple Sequence Alignment of viral genomes

• Authors : Moshiri, Niema

Subjects: COVID-19 (Disease); Viruses

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EPSAPG : a pipeline combining MMseqs2 and PSI-BLAST to quickly generate extensive protein sequence alignment profiles

• Authors : Arab, Issar

Subjects: Biology; Engineering sciences. Technology; Computer. Automation

• Source: Proceedings of the IEEE/ACM 10th International Conference on Big Data Computing, Applications and Technologies (BDCAT'23), December 4–7, 2023, Taormina (Messina), Italy ; 979-84-00-70473-4

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Using Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) to evaluate cross-taxa species susceptibilities to Antimycin-A

• Authors : Carlie LaLone

Subjects: Toxicology (incl. clinical toxicology); SeqAPASS; Species Extrapolation

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