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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

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

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

       -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’.


       The National Center for Biotechnology Information.


       blast(1),        copymat(1),        formatrpsdb(1),         makemat(1),