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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

-B filename
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.

-F filename
Gifile (file containing list of gi's) for use with -B or -L

-L filename
Create an alias file named filename, limiting the sequences searched to those
specified by -F.

-T filename
Set the taxonomy IDs in ASN.1 deflines according to the table in filename.

-V Verbose: check for non-unique string ids in the database

-a Input file is database in ASN.1 format (otherwise FASTA is expected)

-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.

-i filename
Input file(s) for formatting

-l filename
Log file name (default = formatdb.log)

-n str Base name for BLAST files (defaults to the name of the original FASTA file)

-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'.

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