formatdb

formatdb

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formatdb is used to format protein or nucleotide source databases before these databases can be searched by blastall, blastpgp or MegaBLAST.

An example of a formatdb command-line entry:

formatdb -i fastafile -p F -oflat file T

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]