formatdb

FORMATDB(1)                NCBI Tools User's Manual                FORMATDB(1)



NAME
       formatdb - format protein or nucleotide databases for BLAST

SYNOPSIS
       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]

DESCRIPTION
       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.

OPTIONS
       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'.

AUTHOR
       The National Center for Biotechnology Information.

SEE ALSO
       blast(1), copymat(1), formatrpsdb(1), makemat(1),
       /usr/share/doc/blast2/formatdb.html.



NCBI                              2007-10-19                       FORMATDB(1)