D. T. Hoang, "A Systolic Array for the Sequence Alignment Problem," Brown University, Providence, RI, Technical Report CS-92-22, 1992. Home/Search Document Details and Download
Summary Related Articles Check |
This paper is cited in the following contexts:
Massively Parallel Biosequence Analysis - Hughey (1993) (4 citations) (Correct)
....implement dynamic programming with gap penalties. A reimplimentation on the order of BISP or BioScan could place 256 PEs on each chip, and be clocked 3 6 times faster. Splash and PAM are field programmable gate array systems specifically designed for configuration as special purpose co processors [12, 2, 15]. Thus, they provide for the implementation of sequence comparison algorithms in hardware without the need to fabricate new chips for each algorithm. Programming specific algorithms is, unfortunately, time consuming. An edit distance calculation with fixed costs and no gaps required nearly 3000 ....
D. T. Hoang, "A systolic array for the sequence alignment problem," Tech. Rep. CS92 -22, Dept. Computer Science, Brown University, Providence, RI, Apr. 1992.
FPGA Implementation of Systolic Sequence Alignment - Dzung Hoang Department (1992) (1 citation) Self-citation (Hoang) (Correct)
....sequences, however, require more than just the edit distance: a more informative analysis of the similarity, or homology, of the sequences in the form of an alignment is required. In this paper, we describe an implementation of a systolic algorithm A longer version of this paper can be found in [1]. y Supported during Summer 1991 by an NIH Summer Internship and afterwards by an NSF Graduate Fellowship. z Supported by NSF grant MIP 9020570. for computing sequence alignments on SPLASH. Prior to our work, we know of no systolic array for computing sequence alignments. 1.1 Sequence ....
D. T. Hoang, "A Systolic Array for the Sequence Alignment Problem," Brown University, Providence, RI, Technical Report CS-92-22, 1992.
Searching Genetic Databases on Splash 2 - Dzung Hoang (1993) (25 citations) Self-citation (Hoang) (Correct)
....P NAC implementation, the bidirectional systolic array has been ported to the Splash programmable logic array [5] and now the Splash 2 programmable logic array. An extension of the bidirectional array to compute the alignment of two sequences in addition to the edit distance is described in [8,9]. Comparing sequences of lengths m and n requires at least 2 max(m 1; n 1) processors. The number of steps required to compute the edit distance is proportional to the length of the array. In a typical database search, the same source sequence is compared against all sequences in the database. ....
D. T. Hoang, "A Systolic Array for the Sequence Alignment Problem," Brown University, Providence, RI, Technical Report CS-92-22, 1992.
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