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 ...