D. Lopresti, P-NAC: A systolic array for comparing nucleic acid sequences, Computer 20 (1987), no. 7, 81-88.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....arrays can provide the fastest means of running a particular algorithm with very high PE density. However, they are limited to one single algorithm, and thus cannot supply the flexibility necessary to run a variety of algorithms required analyzing DNA, RNA, and proteins, e.g. P NAC, SAMBA, Bioscan [11, 5, 17]. Reconfigurable systems are based on programmable logic such as field programmable gate arrays (FPGAs) e.g. Spalsh 2, Biocellerator [6, 7] or custom designed arrays, e.g. MGAP [3] They are generally slower and have far lower PE densities than special purpose architectures. They are flexible, ....

D. Lopresti. P-nac: A systolic array for comparing nucleic acid sequences. Computer, 20(7):81--88, 1987.

.... mapped onto the PM directly from a systolic array [50] Some types of systolic arrays can be mapped just as directly onto PMs; for example, we produced a straightforward PM simulation of the dynamicprogramming algorithm for the problem of determining the minimum edit distance between two strings [73, 56]. These multiplication and minimum edit distance algorithms are similar in that computation using both can be expressed on a twodimensional (space time) grid with a linear computational wavefront [51] moreover, it appears that any such algorithm can be mapped directly onto a PM. However, we leave ....

....system that supports the requisite particles and collisions, but was not originally expected to lend itself well to fast and e#cient realization using traditional means. Still, the tremendous success of VLSI technology, as well as previous work in using VLSI to implement CA and systolic arrays [102, 50, 56], suggest that an evaluation of VLSI for building PMs is in order. Much like systolic arrays, CA can be realized in hardware as regular arrays, usually one or two dimensional, of locally interconnected, uniform processors. Each such processor needs only to implement the CA s update rule and to ....

D. Lopresti. P-NAC: A systolic array for comparing nucleic acid sequences. IEEE Computer, 20(2):98--99, 1987.

....array of processing elements. A common mapping is to assign one PE to each character of the query string, and then to shift the database through the linear chain of PEs (Figure 2a) performing the computation in 2n Gamma 1 steps on n PEs. Alternate mappings have been used by BioSCAN and by P NAC [22, 29]. A number of parallel architectures have been developed for sequence analysis. In addition to architectures specifically designed for sequence analysis, existing programmable sequential and parallel architectures have been used for solving sequence problems. Single purpose VLSI can provide the ....

....with very high PE density. However, they are limited to a single algorithm, and thus cannot supply the flexibility necessary to run the variety of algorithms required for analyzing DNA, RNA, and proteins. P NAC was the first such machine, and computed edit distance over a four character alphabet [22]. More recent examples, better tuned to the needs of computational biology, include BioScan, BISP and Samba [29, 5, 20] Reconfigurable systems are based on programmable logic such as field programmable gate arrays (FPGAs) or custom designed arrays. They are generally slower and have far lower PE ....

Daniel P. Lopresti. P-NAC: A systolic array for comparing nucleic acid sequences. Computer, 20(7):98-- 99, July 1987.

....(Rigoutsos and Califano, 1993) on the IBM SP 1 and Blaze (Brutlag et al. 1993) on the MasPar MP 1. An extreme solution has been the development of a class of parallel processors designed expressly to compare biopolymer sequences. Examples of these special purpose multiprocessor systems are PNAC (Lopresti, 1987), BISP (Chow et al. 1991) SPLASH (Gokhale et al. 1990) BSYS (Hughey and Lopresti, 1991) bioccelerator 4 (Compugen, 1995) and BioSCAN (White et al. 1991; Singh et al. 1993) Singh et al. A Dynamically Reconfigurable Systolic Array 2 In this paper we describe BioSCAN (Biological Sequence ....

....options and parameters for database searches, and interpretation the search results is given in (Singh et al. 1996) A typical partial result is shown in Fig. 11b. Singh et al. A Dynamically Reconfigurable Systolic Array 13 9 SYSTEM PERFORMANCE COMPARISON Many other special purpose hardware (Lopresti, 1987; Gokhale et al. 1990; Chow et al. 1991; Hughey and Lopresti, 1991; Compugen, 1995) and software (Altschul et al. 1990; Pearson and Lipman, 1988) for the analysis of biosequences have been reported in the literature. The algorithmic differences, degree of programmability, and diversity of ....

Lopresti, D. (1987). P-NAC: A systolic array for comparing nucleic acid sequences. Computer, 20(7):98--99.

....to the input. The system processes 200k words s: this is faster than a solution previously implemented at CNET using 12 Transputers; it has only half of the performance obtained by a system previously developed at IRISA based on 28 custom VLSI chips and two PCB boards. The DNA matching algorithm [Lop87] is the driving application for the PAM developed at the Supercomputing Research Center in Maryland [ABD92] the reported performance is, here again, in excess of that obtained with supercomputers. The Compugen commercial company [Com93] sells the Bioccelerator, a PAM which can be configured as a ....

D. P. Lopresti, P-NAC: A Systolic Array for Comparing Nucleic Acid Sequences, Computer Magazine 20(7):98--99, 1987.

.... efforts in the area of special purpose processing was the Splash highly parallel programmable logic array, developed by Lopresti and colleagues at the Supercomputing Research Center (see Gokhale 1991) This machine evolved out of the Princeton Nucleic Acid Comparator, or P NAC, developed by Lopresti and Lipton (1987). Both of these machines use a highly parallel architecture to calculate multiple similarity values in parallel. Like the Gene Sequence Processor, Splash makes extensive use of field programmable gate arrays to permit rapid prototyping and flexible implementation. Both Splash and P NAC were ....

Lopresti, D. (1987) P-NAC: A Systolic Array For Comparing Nucleic Acid Sequences.

....are dFLASH (Rigoutsos and Califano, 1993) for the IBM SP 1 and Blaze (Brutlag et al. 1993) for the MP 1 from MasPar. A further extreme solution has been the development of a class of parallel processors designed expressly to operate on biosequence data. These efforts have resulted in the PNAC (Lopresti, 1987), BISP (Chow et al. 1991) SPLASH (Gokhale et al. 1990) BSYS (Hughey and Lopresti, 1991) BIOCCELERATOR (Compugen, 1995) and BioSCAN (White et al. 1991; Singh et al. 1993) Algorithms for detecting and measuring similarities between biological sequences have evolved over the last three ....

Lopresti, D. (1987). P-NAC: A systolic array for comparing nucleic acid sequences. Computer, 20(7):98--99.

....gapped sequence comparison, in which the sequences flow through the array in opposite directions, is also occasionally used because query sequence preloading is not required. If the array is not large enough for the complete query, the dynamic programming computation must be partitioned (Lipton Lopresti, 1987). Fine grain parallelism is the method of choice for the special purpose processors, which generally have the highest performance. For anything but a special purpose processor, the coarse grain approach, when a large database is being searched, will be faster, primarily because communication of ....

....(Pearson, 1995a) Single purpose VLSI (SP) Single purpose VLSI can achieve the highest performance on one single algorithm for, typically, prices in the low tens of thousands of dollars. PNAC, a machine for calculating the edit distance over a four character alphabet, was the first such design (Lopresti, 1987). BioSCAN is a fast and exceedingly high density (812 PEs per chip) implementation of a statistical sequence analysis method similar to BLAST, and is available on the Web (http: genome.cs.unc.edu ) Singh et al. 1993) BISP is a hardware implementation of the full Smith Waterman algorithm, ....

Lopresti, D. P. (1987). P-NAC: A systolic array for comparing nucleic acid sequences. Computer, 20 (7), 98--99.

....it has only half of the performance obtained by a system previously developed at IRISA, based on 28 custom VLSI chips and 2 PC boards. Applications of this algorithm include automated mail sorting using OCR scanners, on the fly keyboard spelling corrections, and DNA sequence matching (see [Lop87]) 4.5 Heat and Laplace equations [Vui93] shows how to adapt the classical finite difference method (see [FLS63] to compute solutions of the heat and Laplace equations in n dimensions with help from special purpose hardware. An implementation of the method on P 1 operates with a pipe line depth ....

D.P. Lopresti. P-NAC: A systolic array for comparing nucleic acid sequences. Computer Magazine, 20(7):98--99, 1987.

....it has only half of the performance obtained by a system previously developed at IRISA, based on 28 custom VLSI chips and 2 PC boards. Applications of this algorithm include automated mail sorting using OCR scanners, on the fly keyboard spelling corrections, and DNA sequence matching (see [Lop87]) 4.5 Heat and Laplace equations [Vui93] shows how to adapt the classical finite difference method (see [FLS63] to compute solutions of the heat and Laplace equations in n dimensions with help from special purpose hardware. An implementation of the method on P 1 operates with a pipe line depth ....

D.P. Lopresti. P-NAC: A systolic array for comparing nucleic acid sequences. Computer Magazine, 20(7):98--99, 1987.

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D. Lopresti, P-NAC: A systolic array for comparing nucleic acid sequences, Computer 20 (1987), no. 7, 81-88.

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L 87 D.P. Lopresti: P-NAC: A Systolic Array for Comparing Nucleic Acid Sequences Computer Magazine 20(7):98--99, (1987).

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