GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis.
The article proposes GenDP, a framework of dynamic programming acceleration for genome sequencing analysis. The authors evaluate GenDP on four dynamic programming (DP) kernels including Banded Smith-Waterman (BSW), Chain, Pairwise Hidden Markov Model (PairHMM), and Partial Order Alignment (POA). The...
| Publicado en: | Communications of the ACM Vol. 68; no. 5; pp. 81 - 91 |
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| Autores principales: | , , , , , , , , , , |
| Formato: | Artículo |
| Publicado: |
Association for Computing Machinery
May2025
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| Materias: | |
| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=hlh&AN=184836342&site=ehost-live header: @attributes: shortDbName: hlh uiTerm: 184836342 longDbName: Humanities International Complete uiTag: AN controlInfo: bkinfo: jinfo: jid: 00010782 ACM jtl: Communications of the ACM issn: 00010782 maglogo: N pubinfo: dt: May2025 vid: 68 iid: 5 pid: 68 pub: Association for Computing Machinery artinfo: ui: 184836342 10.1145/3712168 ppf: 81 ppct: 10 formats: tig: atl: GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis. aug: au: Gu, Yufeng Subramaniyan, Arun Dunn, Tim Khadem, Alireza Chen, Kuan-Yu Paul, Somnath Vasimuddin, Mohammad Misra, Sanchit Blaauw, David Narayanasamy, Satish Das, Reetuparna affil: University of Michigan, Ann Arbor, MI, USA, MI, USA Illumina Inc., San Diego, CA, USA University of Michigan, Ann Arbor, MI, USA Intel Corporation, Hilsboro, OR, USA Intel Corporation, Bangalore, KA, India su: Dynamic programming Genomics Nucleotide sequencing Sequence alignment Computer architecture sug: subj: Dynamic programming Genomics Nucleotide sequencing Sequence alignment Computer architecture ab: The article proposes GenDP, a framework of dynamic programming acceleration for genome sequencing analysis. The authors evaluate GenDP on four dynamic programming (DP) kernels including Banded Smith-Waterman (BSW), Chain, Pairwise Hidden Markov Model (PairHMM), and Partial Order Alignment (POA). The design of the DPAx accelerator is discussed and the graph-partitioning algorithm known as DPMap is also described. pubtype: Periodical doctype: Article src: R language: English refInfo: copyright: @attributes: flag: Y dt: @attributes: year: 2025 holdings: @attributes: islocal: N |
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