Formatdb
--------

There is now a separate document describing formatdb (README.formatdb).  Please
refer to it for information on formatting FASTA files for BLAST searches.


Blastall
--------

Blastall may be used to perform all five flavors of blast comparison. One
may obtain the blastall options by executing 'blastall -' (note the dash). A
typical use of blastall would be to perform a blastn search (nucl. vs. nucl.)
of a file called QUERY would be:

blastall -p blastn -d nr -i QUERY -o out.QUERY

The output is placed into the output file out.QUERY and the search is performed
against the 'nr' database.  If a protein vs. protein search is desired,
then 'blastn' should be replaced with 'blastp' etc.

Some of the most commonly used blastall options are:

blastall   arguments:

  -p  Program Name [String]

        Input should be one of "blastp", "blastn", "blastx", "tblastn", or "tblastx".

  -d  Database [String]
    default = nr

        The database specified must first be formatted with formatdb.
        Multiple database names (bracketed by quotations) will be accepted.
        An example would be

                -d "nr est"

        which will search both the nr and est databases, presenting the results as if one
        'virtual' database consisting of all the entries from both were searched.   The
        statistics are based on the 'virtual' database of nr and est. 

  -i  Query File [File In]
    default = stdin

        The query should be in FASTA format.  If multiple FASTA entries are in the input
        file, all queries will be searched.

  -e  Expectation value (E) [Real]
    default = 10.0

  -o  BLAST report Output File [File Out]  Optional
    default = stdout

  -F  Filter query sequence (DUST with blastn, SEG with others) [String]
    default = T

         BLAST 2.0 and 2.1 uses the dust low-complexity filter for blastn and seg for the
         other programs. Both 'dust' and 'seg' are integral parts of the NCBI toolkit
         and are accessed automatically.

         If one uses "-F T" then normal filtering by seg or dust (for blastn)
         occurs (likewise "-F F" means no filtering whatsoever). 

         This options also takes a string as an argument.  One may use such a
         string to change the specific parameters of seg or invoke other filters.
         Please see the "Filtering Strings" section (below) for details.

  -S  Query strands to search against database (for blast[nx], and tblastx).  3 is both, 1 is top, 2 is bottom [Integer]
    default = 3

  -T  Produce HTML output [T/F]
    default = F

  -l  Restrict search of database to list of GI's [String]  Optional

 This option specifies that only a subset of the database should be
 searched, determined by the list of gi's (i.e., NCBI identifiers) in a
 file.  One can obtain a list of gi's for a given Entrez query from
 http://www.ncbi.nlm.nih.gov/Entrez/batch.html.  This file should
 be in the same directory as the database, or in the directory that
 BLAST is called from.

  -U  Use lower case filtering of FASTA sequence [T/F]  Optional
    default = F

        This option specifies that any lower-case letters in the input FASTA file
        should be masked.