July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 12: Hardware and Software Optimizations
Optimized NCBI-BLAST
The source code for NCBI-BLAST is in the public domain, and anyone can modify it
without restriction (ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools). It’s therefore not sur-
prising that there are a number of variants. The rest of this chapter discusses three of
them.
Apple/Genentech BLAST
Macintosh G4 computers have an additional vector processing unit called Velocity-
Engine or Altivec that can process several similar instructions in parallel. Apple
Computer and Genentech collaborated to rewrite portions of NCBI-BLAST to take
advantage of the Altivec processor. These modifications affect the seeding phase of
BLASTN. The result, AG-BLAST, significantly outperforms NCBI-BLAST under cer-
tain conditions.
Table 12-5 shows an experiment in which a Caenorhabditis elegans transcript
(F44B9.10) was searched against the Caenorhabditis briggsae genome using various
word sizes but otherwise default parameters (the hardware is a 550-MHz Power-
Book). For cross-species work, it’s generally a good idea to employ word sizes
slightly smaller than the default 11 to minimize the chance of missing meaningful
similarities. Here, AG-BLAST has a significant speed advantage over NCBI-BLAST.
AG-BLAST also runs faster at very large word sizes, ...
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I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
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I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.