formatdb - format protein or nucleotide databases for BLAST
formatdb [-] [-B filename] [-F filename] [-L filename] [-T filename]
[-V] [-a] [-b] [-e] [-i filename] [-l filename] [-n str] [-o] [-p F]
[-s] [-t str] [-v N]
formatdb must be used in order to format protein or nucleotide source
databases before these databases can be searched by blastall, blastpgp
or MegaBLAST. The source database may be in either FASTA or ASN.1
format. Although the FASTA format is most often used as input to
formatdb, the use of ASN.1 is advantageous for those who are using
ASN.1 as the common source for other formats such as the GenBank
report. Once a source database file has been formatted by formatdb it
is not needed by BLAST. Please note that if you are going to apply
periodic updates to your BLAST databases using fmerge(1), you will need
to keep the source database file.
A summary of options is included below.
- Print usage message
Binary Gifile produced from the Gifile specified by -F. This
option specifies the name of a binary GI list file. This option
should be used with the -F option. A text GI list may be
specified with the -F option and the -B option will produce that
GI list in binary format. The binary file is smaller and BLAST
does not need to convert it, so it can be read faster.
Gifile (file containing list of gi’s) for use with -B or -L
Create an alias file named filename, limiting the sequences
searched to those specified by -F.
Set the taxonomy IDs in ASN.1 deflines according to the table in
-V Verbose: check for non-unique string ids in the database
-a Input file is database in ASN.1 format (otherwise FASTA is
-b ASN.1 database is binary (as opposed to ASCII text)
-e Input is a Seq-entry. A source ASN.1 database (either text
ascii or binary) may contain a Bioseq-set or just one Bioseq. In
the latter case -e should be provided.
Input file(s) for formatting
Log file name (default = formatdb.log)
-n str Base name for BLAST files (defaults to the name of the original
-o Parse SeqID and create indexes. If the source database is in
FASTA format, the database identifiers in the FASTA definition
line must follow the conventions of the FASTA Defline Format.
-p F Input is a nucleotide, not a protein.
-s Index only by accession, not by locus. This is especially
useful for sequence sets like the EST’s where the accession and
locus names are identical. Formatdb runs faster and produces
smaller temporary files if this option is used. It is strongly
recommended for EST’s, STS’s, GSS’s, and HTGS’s.
-t str Title for database file [String]
-v N Break up large FASTA files into ‘volumes’ of size N million
letters (4000 by default). As part of the creation of a volume,
formatdb writes a new type of BLAST database file, called an
alias file, with the extension ‘nal’ or ‘pal’.
The National Center for Biotechnology Information.
blast(1), copymat(1), formatrpsdb(1), makemat(1),