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.