A Protein Sequence Analysis Hardware Accelerator Based on Divergences
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 proce...
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| Format: | Article |
| Language: | English |
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Wiley
2012-01-01
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| Series: | International Journal of Reconfigurable Computing |
| Online Access: | http://dx.doi.org/10.1155/2012/201378 |
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| author | Juan Fernando Eusse Nahri Moreano Alba Cristina Magalhaes Alves de Melo Ricardo Pezzuol Jacobi |
| author_facet | Juan Fernando Eusse Nahri Moreano Alba Cristina Magalhaes Alves de Melo Ricardo Pezzuol Jacobi |
| author_sort | Juan Fernando Eusse |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-f72b6b41eef94064b13400ee184644ec |
| institution | Kabale University |
| issn | 1687-7195 1687-7209 |
| language | English |
| publishDate | 2012-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Reconfigurable Computing |
| spelling | doaj-art-f72b6b41eef94064b13400ee184644ec2025-02-03T01:30:55ZengWileyInternational Journal of Reconfigurable Computing1687-71951687-72092012-01-01201210.1155/2012/201378201378A Protein Sequence Analysis Hardware Accelerator Based on DivergencesJuan Fernando Eusse0Nahri Moreano1Alba Cristina Magalhaes Alves de Melo2Ricardo Pezzuol Jacobi3Electrical Engineering Department, University of Brasilia, Brasilia, DF 70910-900, BrazilSchool of Computing, Federal University of Mato Grosso do Sul, Campo Grande, MS 79070-900, BrazilComputer Science Department, University of Brasilia, Brasilia, DF 70910-900, BrazilUnB Gama School, University of Brasilia, Gama, DF 72405-610, BrazilThe 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.http://dx.doi.org/10.1155/2012/201378 |
| spellingShingle | Juan Fernando Eusse Nahri Moreano Alba Cristina Magalhaes Alves de Melo Ricardo Pezzuol Jacobi A Protein Sequence Analysis Hardware Accelerator Based on Divergences International Journal of Reconfigurable Computing |
| title | A Protein Sequence Analysis Hardware Accelerator Based on Divergences |
| title_full | A Protein Sequence Analysis Hardware Accelerator Based on Divergences |
| title_fullStr | A Protein Sequence Analysis Hardware Accelerator Based on Divergences |
| title_full_unstemmed | A Protein Sequence Analysis Hardware Accelerator Based on Divergences |
| title_short | A Protein Sequence Analysis Hardware Accelerator Based on Divergences |
| title_sort | protein sequence analysis hardware accelerator based on divergences |
| url | http://dx.doi.org/10.1155/2012/201378 |
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