July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 13: NCBI-BLAST Reference
-s [T/F]
Default: Optional
Creates indexes for accessions but not locus names. Must be used in conjunction with the
-o parameter. For many sequences from DDBJ/GenBank/EMBL, the locus name and acces-
sion number are identical and some disk space can be saved by not including redundant
information. In general, locus names are historical relics, so always include
-s.
-t [string]
Default: Optional
The title for a database file. If this parameter isn’t set, the title of the database will be the
name of the FASTA file or the argument of
-n, if it was set. -t lets you use more descriptive
names that you might not want as filenames. For example:
formatdb -i proteins -t "my favorite human proteins"
In the BLAST report, this is reported in the header as:
Database: my favorite human proteins
Using this parameter can be confusing, because backtracking from reports to databases
might be difficult.
-v [integer]
Default: Optional
The maximum number of sequence bases to be created in a volume. Values range from 1 to
2147483647 (2 billion in powers of two). This parameter is useful if the filesystem doesn’t
support large files. Volumes with greater than
[integer] letters are automatically split, and
an alias is created. See Chapter 9 for more information.
-V [T/F]
Default: F ...
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