With reference to Roy Smith's question about Fasta speed, (although
this does not specifically address his question regarding PC's running FASTA),
we recently had the opportunity to test Fasta on a VAX 9000 - 210, and compare
the results to machines currently in our laboratory or accessible to us
(To show relative performance, WordSearch and Find times are also included):
{ all times rounded to the nearest second }
CPU Seconds Ratio
---------------------------- --------------------------
CONVEX VAX CRAY VAX CONVEX/ 8650/ CRAY/
C230 8650 XMP24 9000 9000 9000 9000
Fasta v1.5a + 79 88 28 15 5.3 5.9 1.9
WordSearch GCG 6 + 270 292 na 42 6.4 7.0 -
Find GCG 6 * 205 110 na 19 10.8 5.8 -
na - program not available
+ humraf12 (49 nt) vs GenBank Primate Database (Rel. 65 - 6997 sequences
8,434,211 nt).
* 5aa vs PIR1,PIR2,PIR3 (Rel. 26 - 25,814 sequences 7,348,950 aa)
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Mark A. Gunnell | Internet: gunnell at ncifcrf.gov
Sci. Applications Analyst | Bitnet: gunnell%ncifcrf.gov at cunyvm.bitnet
Advanced Scientific Computing Lab.| Phone: (301) 846-5779
PRI/DynCorp |
NCI-FCRDC |
PO Box B, Bldg 430 |
Frederick, MD 21702 USA |
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