A programmable array processor architecture for flexible approximate string matching algorithms
Journal of Parallel and Distributed Computing
A General Reconfigurable Architecture for the BLAST Algorithm
Journal of VLSI Signal Processing Systems
Single pass streaming BLAST on FPGAs
Parallel Computing
Application development on hybrid systems
Proceedings of the 2007 ACM/IEEE conference on Supercomputing
Visions for application development on hybrid computing systems
Parallel Computing
Mercury BLASTP: Accelerating Protein Sequence Alignment
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
A stream chip-multiprocessor for bioinformatics
ACM SIGARCH Computer Architecture News
Hardware BLAST Algorithms with Multi-seeds Detection and Parallel Extension
ARC '08 Proceedings of the 4th international workshop on Reconfigurable Computing: Architectures, Tools and Applications
Sorting on architecturally diverse computer systems
Proceedings of the Third International Workshop on High-Performance Reconfigurable Computing Technology and Applications
Reconfigurable custom floating-point instructions (abstract only)
Proceedings of the 18th annual ACM/SIGDA international symposium on Field programmable gate arrays
Reducing storage requirements in accelerating algorithm of global BioSequence alignment on FPGA
APPT'07 Proceedings of the 7th international conference on Advanced parallel processing technologies
Fast and accurate NCBI BLASTP: acceleration with multiphase FPGA-based prefiltering
Proceedings of the 24th ACM International Conference on Supercomputing
Design and implementation of a database filter for BLAST acceleration
Proceedings of the Conference on Design, Automation and Test in Europe
A Hardware Viewpoint on Biosequence Analysis: What’s Next?
ACM Journal on Emerging Technologies in Computing Systems (JETC) - Special Issue on Bioinformatics
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Approximate string matching is funda- mental to bioinformatics, and has been the subject of numerous FPGA acceleration studies. We ad- dress issues with respect to FPGA implementations of both BLAST- and dynamic-programming- (DP) based methods. Our primary contributions are two new algo- rithms for emulating the seeding and extension phases of BLAST. These operate in a single pass through a database at streaming rate (110 Maa/sec on a VP70 for query sizes up to 600 and 170 Maa/sec on a Virtex4 for query sizes up to 1024), and with no preprocessing other than loading the query string. Further, they use very high sensitivity with no slowdown. While cur- rent 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.