makemat(1) [debian man page]

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

NAME

       makemat - convert binary profiles into portable ASCII form

SYNOPSIS

       makemat [-] [-E N] [-G N] [-H] [-P filename] [-S X] [-U str] [-d str] [-z N]

DESCRIPTION

       makemat converts a collection of binary profiles, created by the -C option of PSI-BLAST, into portable ASCII form.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -E N   Cost to extend a gap (default = 1)

       -G N   Cost to open a gap (default = 11)

       -H     Print help; overrides all other arguments

       -P filename
	      Database name for profile database (default = stdin)

       -S X   Scaling factor for matrix outputs to avoid round-off problems (default = 100)

       -U str Underlying Matrix (default = BLOSUM62)

       -d str Underlying sequence database used to make profiles (default = nr)

       -z N   Effective length of the profile database (0 for length of -d option)

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       blast(1), copymat(1), /usr/share/doc/blast2/impala.html

NCBI
								    2004-06-25								MAKEMAT(1)

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 scoring 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  inter-
       mediate	files  these  utilities  would	need  to create an RPS Blast database.	Further, scoremat objects are in more general use than the
       binary format 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; default = 1)

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

       -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), /usr/share/doc/blast2/formatrpsdb.html

NCBI
								    2004-10-20							    FORMATRPSDB(1)