An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models.
BMC Bioinformatics
; 25(1): 247, 2024 Jul 29.
Article
em En
| MEDLINE
| ID: mdl-39075359
ABSTRACT
BACKGROUND:
Sequence alignment lies at the heart of genome sequence annotation. While the BLAST suite of alignment tools has long held an important role in alignment-based sequence database search, greater sensitivity is achieved through the use of profile hidden Markov models (pHMMs). Here, we describe an FPGA hardware accelerator, called HAVAC, that targets a key bottleneck step (SSV) in the analysis pipeline of the popular pHMM alignment tool, HMMER.RESULTS:
The HAVAC kernel calculates the SSV matrix at 1739 GCUPS on a â¼ $3000 Xilinx Alveo U50 FPGA accelerator card, â¼ 227× faster than the optimized SSV implementation in nhmmer. Accounting for PCI-e data transfer data processing, HAVAC is 65× faster than nhmmer's SSV with one thread and 35× faster than nhmmer with four threads, and uses â¼ 31% the energy of a traditional high end Intel CPU.CONCLUSIONS:
HAVAC demonstrates the potential offered by FPGA hardware accelerators to produce dramatic speed gains in sequence annotation and related bioinformatics applications. Because these computations are performed on a co-processor, the host CPU remains free to simultaneously compute other aspects of the analysis pipeline.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Cadeias de Markov
/
Alinhamento de Sequência
Idioma:
En
Revista:
BMC Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2024
Tipo de documento:
Article
País de afiliação:
Estados Unidos