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A Protein Sequence Analysis Hardware Accelerator Based on Divergences
Joint Authors
de Melo, Alba Cristina Magalhaes Alves
Eusse, Juan Fernando
Moreano, Nahri
Jacobi, Ricardo Pezzuol
Source
International Journal of Reconfigurable Computing
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-19, 19 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-04-12
Country of Publication
Egypt
No. of Pages
19
Main Subjects
Topics
Abstract EN
The Viterbi algorithm is one of the most used dynamic programming algorithms for protein comparison and identification, based on hidden markov Models (HMMs).
Most of the works in the literature focus on the implementation of hardware accelerators that act as a prefilter stage in the comparison process.
This stage discards poorly aligned sequences with a low similarity score and forwards sequences with good similarity scores to software, where they are reprocessed to generate the sequence alignment.
In order to reduce the software reprocessing time, this work proposes a hardware accelerator for the Viterbi algorithm which includes the concept of divergence, in which the region of interest of the dynamic programming matrices is delimited.
We obtained gains of up to 182x when compared to unaccelerated software.
The performance measurement methodology adopted in this work takes into account not only the acceleration achieved by the hardware but also the reprocessing software stage required to generate the alignment.
American Psychological Association (APA)
Eusse, Juan Fernando& Moreano, Nahri& de Melo, Alba Cristina Magalhaes Alves& Jacobi, Ricardo Pezzuol. 2012. A Protein Sequence Analysis Hardware Accelerator Based on Divergences. International Journal of Reconfigurable Computing،Vol. 2012, no. 2012, pp.1-19.
https://search.emarefa.net/detail/BIM-453978
Modern Language Association (MLA)
Eusse, Juan Fernando…[et al.]. A Protein Sequence Analysis Hardware Accelerator Based on Divergences. International Journal of Reconfigurable Computing No. 2012 (2012), pp.1-19.
https://search.emarefa.net/detail/BIM-453978
American Medical Association (AMA)
Eusse, Juan Fernando& Moreano, Nahri& de Melo, Alba Cristina Magalhaes Alves& Jacobi, Ricardo Pezzuol. A Protein Sequence Analysis Hardware Accelerator Based on Divergences. International Journal of Reconfigurable Computing. 2012. Vol. 2012, no. 2012, pp.1-19.
https://search.emarefa.net/detail/BIM-453978
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-453978