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       formatrpsdb - Build databases for RPS Blast


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


       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.


       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

       -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)


       The National Center for Biotechnology Information.


       blast(1),         copymat(1),         formatdb(1),          makemat(1),