.TH FORMATDB 1 2007-10-19 NCBI "NCBI Tools User's Manual"
.SH NAME
formatdb \- format protein or nucleotide databases for BLAST
.SH SYNOPSIS
.B formatdb
[\|\fB\-\fP\|]
[\|\fB\-B\fP\ \fIfilename\fP\|]
[\|\fB\-F\fP\ \fIfilename\fP\|]
[\|\fB\-L\fP\ \fIfilename\fP\|]
[\|\fB\-T\fP\ \fIfilename\fP\|]
[\|\fB\-V\fP\|]
[\|\fB\-a\fP\|]
[\|\fB\-b\fP\|]
[\|\fB\-e\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-l\fP\ \fIfilename\fP\|]
[\|\fB\-n\fP\ \fIstr\fP\|]
[\|\fB\-o\fP\|]
[\|\fB\-p\ F\fP\|]
[\|\fB\-s\fP\|]
[\|\fB\-t\fP\ \fIstr\fP\|]
[\|\fB\-v\fP\ \fIN\fP\|]
.SH DESCRIPTION
\fBformatdb\fP 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 \fBformatdb\fP, 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
\fBformatdb\fP it is not needed by BLAST. Please note that if you are
going to apply periodic updates to your BLAST databases using
\fBfmerge\fP(1), you will need to keep the source database file.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-B\fP\ \fIfilename\fP
Binary Gifile produced from the Gifile specified by \fB\-F\fP.  This
option specifies the name of a binary GI list file.  This option
should be used with the \fB\-F\fP option.  A text GI list may be
specified with the \fB\-F\fP option and the \fB\-B\fP 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.
.TP
\fB\-F\fP\ \fIfilename\fP
Gifile (file containing list of gi's) for use with \fB\-B\fP or \fB\-L\fP
.TP
\fB\-L\fP\ \fIfilename\fP
Create an alias file named \fIfilename\fP, limiting the sequences
searched to those specified by \fB\-F\fP.
.TP
\fB\-T\fP\ \fIfilename\fP
Set the taxonomy IDs in ASN.1 deflines according to the table in
\fIfilename\fP.
.TP
\fB\-V\fP
Verbose: check for non-unique string ids in the database
.TP
\fB\-a\fP
Input file is database in ASN.1 format (otherwise FASTA is expected)
.TP
\fB\-b\fP
ASN.1 database is binary (as opposed to ASCII text)
.TP
\fB\-e\fP
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 \fB\-e\fP should be provided.
.TP
\fB\-i\fP\ \fIfilename\fP
Input file(s) for formatting
.TP
\fB\-l\fP\ \fIfilename\fP
Log file name (default = \fBformatdb.log\fP)
.TP
\fB\-n\fP\ \fIstr\fP
Base name for BLAST files (defaults to the name of the original FASTA file)
.TP
\fB\-o\fP
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.
.TP
\fB\-p\ F\fP
Input is a nucleotide, not a protein.
.TP
\fB\-s\fP
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.
.TP
\fB\-t\fP\ \fIstr\fP
Title for database file [String]
.TP
\fB\-v\fP\ \fIN\fP
Break up large FASTA files into `volumes' of size \fIN\fP million
letters (4000 by default).  As part of the creation of a volume,
\fBformatdb\fP writes a new type of BLAST database file, called an
alias file, with the extension `nal' or `pal'.
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.BR blast (1),
.BR copymat (1),
.BR formatrpsdb (1),
.BR makemat (1),
/usr/share/doc/blast2/formatdb.html.