README for netblast (network-client BLAST)
			last updated 6/14/99


	This README describes the BLAST client (blastcl3), which accesses the
newest NCBI BLAST search engine (version 2.0).  The software behind BLAST version 
2.0 was written from scratch to allow BLAST to handle the new challenges posed 
by the sequence databases in the coming years.  Updates to this software will
continue in the coming years.

	Blastcl3 can search all the sequences in a FASTA file, produce one-to-many
(master-slave) alignments as well as HTML, and it can perform searches against multiple
databases.  Organism-specific searches are planned for the near future.  A full list of 
command-line options is given below.

	Blastcl3 should be used instead of previous clients such as blastcl2, 
blastcli, and PowerBlast.  (Blastcl2 and blastcli do not produce gapped alignments 
at all; PowerBlast performs the gapped computation on the user machine, instead of 
the NCBI server).  The service that these older clients use will not be supported 
indefinitely.

	The setup for NCBI network clients has been greatly simplified.  If you are
not behind a firewall no further action is required.  If you are behind a firewall,
and already use Sequin or Entrez, or if your system administrator has already performed
the setup, then you should be able to start performing searches immediately.  Otherwise,
please refer to 'firewall.txt' that is included with this archive.  Follow the instructions
for "Configuring newer clients".  

	Please send questions and comments to 'blast-help@ncbi.nlm.nih.gov'.

Blastcl3
--------

Blastcl3 may be used to perform all five flavors of blast comparison. One
may obtain the blastcl3 options by executing 'blastcl3 -' (note the dash). A
typical use of blastcl3 would be to perform a blastn search (nucl. vs. nucl.) 
of a file called QUERY:

blastcl3 -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 blastcl3 options are:

blastcl3   arguments:

  -p  Program Name [String]

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

  -d  Database [String]
    default = nr

        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) [T/F]
    default = T

         BLAST 2.0 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).  The seg options
         can be changed by using:

         -F "S 10 1.0 1.5"

         which specifies a window of 10, locut of 1.0 and hicut of 1.5.  A coiled-coiled filter,
         based on the work of Lupas et al. (Science, vol 252, pp. 1162-4 (1991)) and written by
         John Kuzio (Wilson et al., J Gen Virol, vol. 76, pp. 2923-32 (1995)), may be invoked
         by specifying:

         -F "C"

         There are three parameters for this: window, cutoff (prob of a coil-coil), and
         linker (distance between two coiled-coiled regions that should be linked
         together).  These are now set to

         window: 22
         cutoff: 40.0
         linker: 32

         One may also change the coiled-coiled parameters in a manner analogous to
         that of seg:

         -F "C 28 40.0 32" will change the window to 28.

         One may also run both seg and coiled-coiled together by using a ";":

         -F "C;S"

         Filtering by dust may also be specified by:

         -F "D"

         It is possible to specify that the masking should only be done during
         the process of building the initial words by starting the filtering
         command with 'm':

         -F "m S"

         which specifies that seg (with default arguments) should be used for masking, 
         but that the masking should only be done when the words are being built.  
         This masking option is available with all filters.

  -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