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FORMATRPSDB(1)		   NCBI	Tools User's Manual		FORMATRPSDB(1)

NAME
       formatrpsdb - Build databases for RPS Blast

SYNOPSIS
       formatrpsdb  [-]	 [-E N]	[-G N] [-S X] [-U str] [-b] [-f	X] -i filename
       [-l filename] [-n str] [-o] [-t str] [-v	N]

DESCRIPTION
       Formatrpsdb is a	utility	that converts a	collection of input  sequences
       into  a	database suitable for use with Reverse Position	Specific (RPS)
       Blast.  Each input sequence, together with its position-specific	 scor-
       ing  matrix  (PSSM),  is	 ASN.1	encoded	 into a	PssmWithParameters (or
       `scoremat') object and resides in a separate  file.   Scoremat  objects
       can  be	created	 using blastpgp.  Formatrpsdb is given a list of these
       files and produces the corresponding database.

       Formatrpsdb is designed to perform the work of  formatdb,  makemat  and
       copymat simultaneously, without generating the large number of interme-
       diate files these utilities would need to create	an RPS Blast database.
       Further,	 scoremat objects are in more general use than the binary for-
       mat makemat requires.  It is hoped that direct manipulation of scoremat
       objects	will encourage conversion of more diverse sequence collections
       into RPS	Blast databases.

       Databases generated by formatrpsdb are binary compatible	with databases
       generated by formatdb/makemat/copymat, although the database files will
       in general not be byte- for-byte	identical.

OPTIONS
       A summary of options is included	below.

       -      Print usage message

       -E N   The gap extension	penalty	(if not	specified in the scoremat; de-
	      fault = 1)

       -G N   The  gap	opening	penalty	(if not	specified in the scoremat; de-
	      fault = 11)

       -S X   For scoremats that contain only residue frequencies, the scaling
	      factor to	apply when creating PSSMs (default = 100)

       -U str Underlying  score	 matrix	(if not	specified in the scoremat; de-
	      fault = BLOSUM62)

       -b     Scoremat files are binary	(vs. text) ASN1.

       -f X   Threshold	for extending hits for RPS database (default = 11)

       -i filename
	      Input file containing list of ASN.1 Scoremat filenames

       -l filename
	      Log file name (default = formatrpsdb.log)

       -n str Base name	of output database (same as input file if  not	speci-
	      fied)

       -o     Create index files for database

       -t str Title for	database file

       -v N   Database	volume size in millions	of letters (default = 0, which
	      really means no limit)

AUTHOR
       The National Center for Biotechnology Information.

SEE ALSO
       blast(1), copymat(1), formatdb(1), makemat(1), formatrpsdb.html

NCBI				  2004-10-20			FORMATRPSDB(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO

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