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 intermediate 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