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International Parallel and Distributed Processing Symposium (IPDPS'03)
Sequence Alignment on the Cray MTA-2
Nice, France
April 22-April 26
ISBN: 0-7695-1926-1
ASCII Text
x 
 
Shahid H. Bokhari, Jon R. Sauer, "Sequence Alignment on the Cray MTA-2," Parallel and Distributed Processing Symposium, International, pp. 152a, International Parallel and Distributed Processing Symposium (IPDPS'03), 2003.
 
 
BibTex
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@article{ 10.1109/IPDPS.2003.1213285,
author = {Shahid H. Bokhari and Jon R. Sauer},
title = {Sequence Alignment on the Cray MTA-2},
journal ={Parallel and Distributed Processing Symposium, International},
volume = {0},
year = {2003},
issn = {1530-2075},
pages = {152a},
doi = {http://doi.ieeecomputersociety.org/10.1109/IPDPS.2003.1213285},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - CONF
JO - Parallel and Distributed Processing Symposium, International
TI - Sequence Alignment on the Cray MTA-2
SN - 1530-2075
SP
EP
A1 - Shahid H. Bokhari,
A1 - Jon R. Sauer,
PY - 2003
KW - null
VL - 0
JA - Parallel and Distributed Processing Symposium, International
ER -
 
Shahid H. Bokhari, University of Engineering & Technology
Jon R. Sauer, Eagle Research & Development
The standard algorithm for alignment of DNA sequences using dynamic programming has been implemented on the Cray MTA-2 (Multithreaded Architecture-2) at ENRI (Electronic Navigation Research Institute), Japan. Descriptions of several variants of this algorithm and their measured performance are provided. It is shown that the use of "Full/Empty" bits (a feature unique to the MTA) leads to implementations that provide almost perfect speedup for large problems on 1-8 processors. These results demonstrate the potential power of the MTA and emphasize its suitability for bioinformatic and dynamic programming applications.
Citation:
Shahid H. Bokhari, Jon R. Sauer, "Sequence Alignment on the Cray MTA-2," ipdps, pp.152a, International Parallel and Distributed Processing Symposium (IPDPS'03), 2003
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