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AG-BLAST does have a few disadvantages. First, the version may be slightly out of
date with respect to NCBI-BLAST. The current version of AG-BLAST is based on
2.2.2, while NCBI-BLAST is up to Version 2.2.6. Not all changes are backward-
compatible; for example, the latest preformatted databases require Version 2.2.5.
Second, AG-BLAST doesn’t work with multiple CPUs. You can execute more than
one job at a time, but you can’t use the -a option to increase the number of CPUs
used by a single process. Finally, the minimum word size on AG-BLAST is 8, or
one greater than the NCBI-BLAST minimum. See http://developer.apple.com/
hardware/ve/acgresearch.html for more information.
Paracel-BLAST and BlastMachine
Paracel makes an NCBI-BLAST derivative called Paracel-BLAST and sells it with a
prepackaged computer cluster called a BlastMachine. This product takes all the high
performance hardware and software tricks and puts them into a single, easy-to-use
product. The hardware is a rack of Linux-Intel machines, and the DRM software is
Platform LSF. Large query sequences are chopped, small ones are packed, and data is
distributed so the search comes back as fast as possible. This is really convenient
because it lets users concentrate on what they want to do and not how they have to
do it. In the end, more science and less frustration is a good thing.
See http://www.paracel.com for more information.
TimeLogic uses an entirely different approach to optimizing BLAST. The BLAST
algorithm is soft-wired into a special kind of chip called a field programmable gate
array (FPGA). Each FPGA executes the search very quickly and multiple FPGA
boards reside in a single computer called a DeCypher accelerator. The end result is a
specialized computer that is limited in what it can do, but what it does, it does aston-
ishingly well. A single DeCypher accelerator running Tera-BLAST (the name for their
Table 12-5. Apple/Genentech BLAST
W NCBI-BLAST (sec) AG-BLAST (sec) Speed increase
8 56.9 37.9 1.5 x
9 50.0 9.5 5.3 x
10 46.6 5.5 8.5 x
11 2.9 2.8 1.0 x
15 2.1 2.1 1.0 x
20 1.4 1.0 1.4 x
30 1.4 0.6 2.3 x
40 1.4 0.5 2.8 x