Publications by authors named "Bharat Sukhwani"

3 Publications

  • Page 1 of 1

Single Pass Streaming BLAST on FPGAs.

Parallel Comput 2007 Nov;33(10-11):741-756

Department of Electrical and Computer Engineering, Boston University; Boston, MA 02215, Web: http://www.bu.edu/caadlab .

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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http://dx.doi.org/10.1016/j.parco.2007.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2598392PMC
November 2007

Computing Models for FPGA-Based Accelerators.

Comput Sci Eng 2008 Oct;10(6):35-45

Boston University.

Field-programmable gate arrays are widely considered as accelerators for compute-intensive applications. A critical phase of FPGA application development is finding and mapping to the appropriate computing model. FPGA computing enables models with highly flexible fine-grained parallelism and associative operations such as broadcast and collective response. Several case studies demonstrate the effectiveness of using these computing models in developing FPGA applications for molecular modeling.
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http://dx.doi.org/10.1109/MCSE.2008.143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3096930PMC
October 2008

Achieving High Performance with FPGA-Based Computing.

Computer (Long Beach Calif) 2007 Mar;40(3):50-57

Boston University.

Numerous application areas, including bioinformatics and computational biology, demand increasing amounts of processing capability. In many cases, the computation cores and data types are suited to field-programmable gate arrays. The challenge is identifying the design techniques that can extract high performance potential from the FPGA fabric.
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http://dx.doi.org/10.1109/MC.2007.79DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098506PMC
March 2007
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