BLAST

This is the Title of the Book, eMatter Edition

Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.

CPUs and Computer Architecture

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The problem with the first pipeline is that if the BLAST databases are large, they may

not all be cached. Each BLAST database can bump out the previously cached file if

you don’t have enough RAM, and then you get no benefit from caching. The second

structure keeps the same BLAST database in memory for all the sequences. Before

you tear apart your current pipeline, however, remember that caching isn’t going to

help much with sensitive searches. If most of your searches are sensitive, it is a waste

of effort to optimize the already fast parts of your pipeline. As in any tuning proce-

dure, optimize the major bottlenecks first.

CPUs and Computer Architecture

The clock speed of a CPU isn’t necessarily an accurate indicator of how fast it will

run BLAST. There are other complicating factors such as the amount of L2 cache,

the memory latency and the speed of the front-side bus. Unfortunately, there is no

good rule to predict how fast BLAST will perform on a particular computer except

for the obvious within-family predictions—for example, that a 1-GHz Pentium III

will be faster than an 800-MHz Pentium III. The best you can do is to benchmark a

bunch of systems or contact people who have already done so.

Two benchmarks are provided Table 12-3. Before reading the description, please

understand that you should use extreme caution whenever interpreting any bench-

marks because the benchmarking protocol may be very different from your everyday

tasks, and therefore may not reflect real-world performance. The best benchmark

procedure should mimic your daily routine. In addition, if you use benchmarks to

decide what hardware to purchase, you may be in for a nasty surprise, as other

important considerations may override a simplistic interpretation of the “most

BLAST for the buck.” Total cost of ownership is a complicated equation that

includes maintenance, support, facilities, cooling, and interfacing with legacy equip-

ment and culture.

Table 12-2 shows the performance on various platforms when searching all mem-

bers of a database against themselves. There are two databases, and both can be

found at http://examples.oreilly.com/BLAST. The tests were performed using default

parameters for NCBI-BLAST. The following command lines were used:

time blastall -p blastn -d ESTs -i ESTs > /dev/null

time blastall -p blastp -d globins -i globins > /dev/null

Table 12-2. Performance benchmarks of various systems

CPU; clock speed blastn test blastp test

Time (sec) Giga-cycles Time (sec) Giga-cycles

Macintosh G4: 550 MHz 1011 556 1599 879

Sun Ultra Sparc III; 750 MHz 835 626 1427 1070

Intel Pentium III; 1 GHz 649 649 1187 1187