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

ABSTRACT:

Motivation

Recent advances in sequencing technologies have stressed the critical role of sequence analysis algorithms and tools in genomics and healthcare research. In particular, sequence alignment is a fundamental building block in many sequence analysis pipelines and is frequently a performance bottleneck both in terms of execution time and memory usage. Classical sequence alignment algorithms are based on dynamic programming and often require quadratic time and memory with respect to the sequence length. As a result, classical sequence alignment algorithms fail to scale with increasing sequence lengths and quickly become memory-bound due to data-movement penalties.

Results

Processing-In-Memory (PIM) is an emerging architectural paradigm that seeks to accelerate memory-bo

SUBMITTER: Alonso-Marin A 

PROVIDER: S-EPMC11576351 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature