Single pass streaming BLAST on FPGAs
Approximate string matching is fundamental to bioinformatics and has been the subject of numerous FPGA acceleration studies. We address issues with respect to FPGA implementations of both BLAST- and dynamic-programming- (DP) based methods. Our primary contribution is a new algorithm for emulating th...
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| Published in: | Parallel computing Vol. 33; no. 10; pp. 741 - 756 |
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| Main Authors: | , , , , |
| Format: | Journal Article |
| Language: | English |
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Elsevier B.V
01.11.2007
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| ISSN: | 0167-8191, 1872-7336 |
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| Abstract | Approximate string matching is fundamental to bioinformatics and has been the subject of numerous FPGA acceleration studies. We address issues with respect to FPGA implementations of both BLAST- and dynamic-programming- (DP) based methods. Our primary contribution is a new algorithm for emulating the seeding and extension phases of BLAST. This operates in a single pass through a database at streaming rate, and with no preprocessing other than loading the query string. Moreover, it emulates parameters turned to maximum possible sensitivity with no slowdown. While current DP-based methods also operate at streaming rate, generating results can be cumbersome. We address this with a new structure for data extraction. We present results from several implementations showing order of magnitude acceleration over serial reference code. A simple extension assures compatibility with NCBI BLAST. |
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| AbstractList | Approximate string matching is fundamental to bioinformatics and has been the subject of numerous FPGA acceleration studies. We address issues with respect to FPGA implementations of both BLAST- and dynamic-programming- (DP) based methods. Our primary contribution is a new algorithm for emulating the seeding and extension phases of BLAST. This operates in a single pass through a database at streaming rate, and with no preprocessing other than loading the query string. Moreover, it emulates parameters turned to maximum possible sensitivity with no slowdown. While current DP-based methods also operate at streaming rate, generating results can be cumbersome. We address this with a new structure for data extraction. We present results from several implementations showing order of magnitude acceleration over serial reference code. A simple extension assures compatibility with NCBI BLAST. Approximate string matching is fundamental to bioinformatics and has been the subject of numerous FPGA acceleration studies. We address issues with respect to FPGA implementations of both BLAST- and dynamic-programming- (DP) based methods. Our primary contribution is a new algorithm for emulating the seeding and extension phases of BLAST. This operates in a single pass through a database at streaming rate, and with no preprocessing other than loading the query string. Moreover, it emulates parameters turned to maximum possible sensitivity with no slowdown. While current DP-based methods also operate at streaming rate, generating results can be cumbersome. We address this with a new structure for data extraction. We present results from several implementations showing order of magnitude acceleration over serial reference code. A simple extension assures compatibility with NCBI BLAST.Approximate string matching is fundamental to bioinformatics and has been the subject of numerous FPGA acceleration studies. We address issues with respect to FPGA implementations of both BLAST- and dynamic-programming- (DP) based methods. Our primary contribution is a new algorithm for emulating the seeding and extension phases of BLAST. This operates in a single pass through a database at streaming rate, and with no preprocessing other than loading the query string. Moreover, it emulates parameters turned to maximum possible sensitivity with no slowdown. While current DP-based methods also operate at streaming rate, generating results can be cumbersome. We address this with a new structure for data extraction. We present results from several implementations showing order of magnitude acceleration over serial reference code. A simple extension assures compatibility with NCBI BLAST. |
| Author | Herbordt, Martin C. Sukhwani, Bharat Gu, Yongfeng VanCourt, Tom Model, Josh |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/19081828$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1016/S0022-2836(05)80360-2 10.1109/FCCM.2006.64 10.1109/ASAP.1991.238887 10.1007/978-3-540-30117-2_5 10.1007/978-3-540-45234-8_37 10.1093/nar/25.17.3389 10.1109/ASAP.2000.862401 10.1109/FCCM.2007.11 10.1016/j.micpro.2006.04.001 10.1109/ASAP.2004.1342485 10.1007/3-540-46117-5_133 10.1126/science.2717944 10.1109/FPGA.1993.279464 10.1109/ASAP.1994.331791 10.1109/MC.1987.1663629 |
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| Title | Single pass streaming BLAST on FPGAs |
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