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Chapter 14: WU-BLAST Reference
-M [number]
Default: 96m
Sets the cache size for indexing. For faster indexing, the size may be increased (for example,
-M 512m).
-O [4..8]
Default: 4
Sets the number of bytes of precision. The default value allows databases of up to 4 billion
amino acids or 16 billion nucleotides. If you expect a database to contain more than this
limit, increasing precision by one level multiplies the limit by 256. Setting
-O is necessary
only if you append to the database because the precision automatically increases appropri-
ately when databases are created.
-P [integer]
Default: 60
This option applies only when dumping the entire content of a database with -r. -P
controls the length of the sequence lines; -P 0 puts the whole sequence on one line.
See also
-r
-q [0..3]
Default: 0
Certain files may contain numerous nonfatal errors in their identifier format. -q quiets
these errors.
0 No silencing
1 Silences field1 errors
2 Silences field 2 errors
3 Silences all fields
-r
Default: Off
Reports (dumps) the entire database content to stdout in FASTA format.
-T [string]
Default: Off
This option lets you restrict indexing of identifiers to a particular database name or tag.
The [string] has two parts: part 1 is the name of the database (e.g.,
gb for GenBank or emb
for EMBL—see Chapter 10), and part 2 is either blank or a number.