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.