July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 10: Installation and Command-Line Tutorial
The behavior of WU-BLAST on multiprocessor systems is worth discussing, and if
you’re one of the lucky people who have access to a computer with 16 processors or
more, /etc/sysblast will definitely help you. WU-BLAST lets users control the num-
ber of CPUs with the –cpus command-line parameter. If this parameter isn’t given an
explicit value, the programs uses all the processors in the computer (except for
BLASTN, which reins itself in at four processors). While this may be good for BLAST
users, your other users may not be so happy. This is where the /etc/sysblast file is crit-
ical because it allows you to modify the default behavior and set limits for CPU
usage.
Command-Line Tutorial
Now that you’ve installed the NCBI-BLAST and/or WU-BLAST software, it’s time to
try it out. To do this, you will need sequences for both queries and databases. It’s
generally a good idea to start with something small and make sure it works before
attempting to analyze large databases. To begin, download the book’s example files
from http://examples.oreilly.com/BLAST. Copy the Sequence directory to a local hard
disk. This directory contains several database and sequences in FASTA format. The
six files you will need for testing are described in Table ...
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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.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
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.