J. D. Hirschberg, R. Hughley, and K. Karplus. Kestrel: a programmable array for sequence analysis. In Proc. of IEEE Int'l Conf. on Application-specific Systems, Architecture, and Processors, 1996.  Home/Search   Document Details and Download   Summary   Related Articles   Check

....via the accelerator. Performing sequence comparison on a systolic array is not a new idea. Other systems based on these structures have been described in the literature. Related projects using a dedicated systolic array are the Bisp [4] and the BioScan [13] machines. Other machines, Kestrel [7] or Rapid 2 [2] are based on a programmable systolic array. fpga systems like Splash 2 [8] or PeRLe 1 [6] used custom systolic arrays for sequence comparison. Thus, 5 disk storage host workstation reconfigurable interface linear systolic array FPGA memory full custom VLSI processors Dec ....

J.D. Hirschberg, R. Hughey, and K. Karplus, KESTREL: A Programmable Array for Sequence Analysis. in IEEE Computer Society Press, ASAP'96, Chicago, Illinois, August 1996, pp: 25--34.

....5 Controller Northern Board RAM Northern Western Western Board RAM Interface Processors Interface Processors PC Bus Figure 5. 9 Architecture of the Systola 1024 architecture neural networks; ii) Synapse 1, designed by Siemens [40] another systolic architecture for neural networks; iii) Kestrel [41], a programmable systolic architecture dedicated to Dna processing; iv) MicMacs [42, 43] a programmable systolic array for string matching algorithms; v) movie [44] and Sympathy2 [45] designed for image processing applications. 5.3.3 Reconfigurable architectures Another popular approach for ....

J. Hirschberg, R. Hughey, and K. Karplus, "KESTREL: A Programmable Array for Sequence Analysis," in ASAP'96 (I. C. S. Press, ed.), (Chicago, Illinois), pp. 25--34, Aug. 1996. Emerging Technologies 35

....[11] Performing sequence comparisons on a systolic array is not a new idea. Other systems based on these structures have been described in the literature. Related projects that have used dedicated systolic arrays are the Bisp [4] and the BioScan [13] machines. Other machines, such as Kestrel [7] or Rapid 2 [2] are based on a programmable systolic array. fpga (field programmable gate array) systems like Splash 2 [8] and PeRLe 1 [6] use custom systolic arrays for sequence comparison. Thus, the general architecture of Samba cannot Query Sequence Database column emulation Figure 3: Samba ....

J.D. Hirschberg, R. Hughey, and K. Karplus, KESTREL: A Programmable Array for Sequence Analysis. in IEEE Computer Society Press, ASAP'96, Chicago, Illinois, August 1996, pp: 25--34.

No context found.

Jerey D. Hirschberg, Richard Hughey, Kevin Karplus, and Don Speck. Kestrel: A programmable array for sequence analysis. In Application-Speci c Array Processors, pages 25-34, Los Alamitos, CA, July 1996. IEEE Computer Society.

.... in the international Human Genome Project [8] development of the gene finding software chosen to annotate the human and Drosophila (fly) genomes [9] success in international protein structure prediction contests [10] 11] and creation of a SIMD programmable accelerator for sequenceanalysis [12]. Since the introduction of our first bioinformatics course in 1996, we have trained many students with majors in Computer Science, Computer Engineering, Mathematics, Molecular, Cell and Developmental (MCD) Biology, Chemistry, and Biochemistry. These students are in very high demand in industry ....

J. D. Hirschberg, D. Dahle, K. Karplus, D. Speck, and R. Hughey, "Kestrel: A programmable array for sequence analysis," Journal of VLSI Signal Processing, vol. 19, pp. 115--126, 1998.

.... configuration as a linear array is ideal for such target applications as sequence analysis, at the same time that it provides a simpler and more flexible programming model than more complex multiple instruction, multiple data stream (MIMD) machines would when applied to the same domain of problems [7]. For the applications that we were envisioning, programmability was more important than large local memories or reconfigurable interconnection fabrics [4] We believe our SIMD approach to be a more cost effective solution than systems using fully reconfigurable general purpose multiprocessors ....

....puts a specific limit of 256 words to its addressable memory. Second, the size of the SRAM was determined by the best possible tradeoff between number of PEs per chip and the size of local memory. For most of the target sequence analysis applications 256 bytes of memory per PE seemed to be enough [7]. Second Generation Kestrel In order to increase the performance of the current system our research group has started the design and implementation of the second generation Kestrel SIMD computer. Due to the large cost associated with the design and fabrication of custom PE chips, the new system ....

J. D. Hirschberg, R. Hughey, K. Karplus, and D. Speck. Kestrel: A programmable array for sequence analysis. IEEE Proc. Int. Conf Application-Specific Systems, Architectures, and Processors, August 1996.

....low precision arithmetic, early introduction of dividends, and simple yet good initial reciprocal estimates. 1. Introduction This paper presents a study of division on an 8 bit processor. It is motivated by the Kestrel architecture, an 8 bit parallel processor tuned to sequence analysis [8]. The word size is a natural choice for sequence analysis applications: characters may require 2 (DNA and RNA) 5 (protein) or 8 (text) bits, and the dynamic programming calculation at the core of many analysis methods requires a mix of precisions including 8 bits for character costs and 24 to 32 ....

J. D. Hirschberg, R. Hughey, K. Karplus, and D. Speck. Kestrel: A programmable array for sequence analysis. In Proc. Int. Conf. Application Specific Array Processors, pages 25--34, Los Alamitos, CA, July 1996. IEEE CS.

No context found.

J. D. Hirschberg, R. Hughley, and K. Karplus. Kestrel: a programmable array for sequence analysis. In Proc. of IEEE Int'l Conf. on Application-specific Systems, Architecture, and Processors, 1996.

Online articles have much greater impact   More about CiteSeer.IST   Add search form to your site   Submit documents   Feedback  

CiteSeer.IST - Copyright Penn State and NEC