xenial (1) formatrpsdb.1.gz

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