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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 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

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