formatdb is used to format protein or nucleotide source databases before these databases can be searched by blastall, blastpgp or MegaBLAST.
The following table summarizes the formatdb options.
| Option | Definition | Type | Default |
| -a | Input file is database in ASN.1 format (otherwise FASTA is expected). | [T/F] | F |
| -b | ASN.1 database in binary mode: - T = Binary.
- F = Text mode.
| [T/F] | F |
| -e | Input is a Seq-entry. | [T/F] | F |
| -i | Input file for formatting (this parameter must be set). | [File In] | |
| -l | Logfile name. | [File Out] | formatdb.log |
| -n | Base name for BLAST files. | [String] | |
| -o | Parse options: - T = True: Parse SeqId and create indexes.
- F = False: Do not parse SeqId. Do not create indexes.
| [T/F] | F |
| -p | Type of file: - T = Protein.
- F = Nucleotide.
| [T/F] | T |
| -s | Create indexes limited only to accessions - sparse. | [T/F] | F |
| -t | Title for database file. | [String] | |
| -v | Number of sequence bases to be created in the volume. | [Integer] | 0 |
| -A | Create ASN.1 structured deflines. | [T/F] | F |
| -B | Binary GIfile produced from the GIfile. This option should be used with the -F option. | [File Out] | |
| -F | GIfile (file containing list of GIs). | [File In] | |
| -L | Create an alias file with this name. | [File Out] | |