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Specifies an output log file. Log messages are appended to this file.
Creates an alias database, which has several uses. It can be a simple synonym for another
database, a selection of specific records from a database (see the
-F option), or a static
virtual database. Alias databases have the .pal or .nal extension, depending on whether they
are proteins or nucleotides.
To create an alias database with a selected set of GI numbers:
formatdb -i db -F gi_list -L alias_name -p [T/F]
To merge databases, first create a synonymous alias and then edit it to include additional
database names. Chapter 11 covers this process in more detail.
Default: Optional, required with -i stdin
Sets the base name for the BLAST database. If not specified, the name of the FASTA file
will be used. If the input is from stdin, this parameter must be set.
Creates indexes. Indexing the databases isn’t required but is recommended. Alias data-
bases that use GI lists (see
-F and -L options) and the blastall -l option require indexed
databases. Additionally, some blastall output options specified with the
require indexing. Indexing adds four files with extensions .nnd, .nni, .nsd, and .nsi for
nucleotides and .pnd, .pni, .psd, and .psi for proteins. If you know you don’t need indexes,
you can save space by omitting
If GI numbers are included and more than one sequence has the same GI number,
formatdb terminates with an error. If accession numbers aren’t unique, an error won’t be
Specifies the type of type of file being formatted. By default, formatdb assumes the file is
protein, so you must set
-p F whenever you format nucleotide databases.