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
Environment variables
Now it’s time to make sure the environment variables function correctly. To start,
move to any random directory on your system and attempt one of the previous
searches, substituting the correct path to the query file:
If the executable path is incorrect, you will see an error message such as:
blastp: command not found
If the databases can’t be found, WU-BLAST reports:
FATAL: Could not open the database: <database name>
WU-BLAST offers informative messages when it fails to find scoring matrices and
complexity filters:
FATAL: "No such file or directory" error encountered (errno=2), when attempting to
FIND the requested sequence filter program "nseg". Please check the setting of the
BLASTFILTER or WUBLASTFILTER environment variables and the permissions on the
program.
EXIT CODE 32
FATAL: Could not find or open a substitution matrix file named: BLOSUM62. Check
file access permissions or the setting of the WUBLASTMAT
(BLASTMAT) environment variable.
EXIT CODE 8
For a complete list of errors and messages, see Chapter 14.
Editing Scoring Matrices
The amino scoring matrix files distributed with NCBI-BLAST and WU-BLAST assign
a score of +1 to paired stop codons. This doesn’t make much biological sense and
reduces the ability ...
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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.