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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...

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Published in:Communications of the ACM Vol. 68; no. 5; pp. 81 - 91
Main Authors: Gu, Yufeng, Subramaniyan, Arun, Dunn, Tim, Khadem, Alireza, Chen, Kuan-Yu, Paul, Somnath, Vasimuddin, Mohammad, Misra, Sanchit, Blaauw, David, Narayanasamy, Satish, Das, Reetuparna
Format: Article
Published: Association for Computing Machinery May2025
Subjects:
Dynamic programming
Genomics
Nucleotide sequencing
Sequence alignment
Computer architecture
Online Access:View this record in EBSCOhost
Summary: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.