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Controlling the scan

SCANPS has a series of different MODEs. Each mode does a different job. Note that not all of the modes shown here are in Version 2.3.9, but are discussed for the sake of completeness (they may come back in future releases).

MODE 0	Scan protein sequence against protein sequence database
	with simple gap penalty.  Default and fastest method.
MODE 2	As for MODE 1, but with Affine gaps.
MODE 20 DNA vs protein database with frameshifts (simple gaps).
MODE 22 DNA vs protein database scan with frameshifts (affine gaps).
MODE 99 Build scanps binary database files from FASTA or PIR format files.
MODE 100 Extract sequences from database (reads output of earlier scan).

In Version 2.3.2 two new modes are introduced:

MODE 200 is like MODE 0 but does iterative searching.
MODE 202 is like MODE 2 but does iterative searching.

MODES 200 and 202 will replace MODE 0 and 2 in a future release of SCANPS.

There are a variety of controlling commands that affect the scan and the output. By default, all results are printed to stdout. You can override this by using the STDOUT command to specify a different file for output. STDERR can also be redefined.

Commands affecting the scan - look in the file scanps_alias.dat to see alternative names for these commands and see APPENDIX II for a full list of commands:

QSEQ_FILE  	is the query sequence file
qseq_format 	defines the format (0 for pir, 1 for fasta)
bdb_root	defines the root name of the binary database to search
ld_pen		length dependent gap-penalty
li_pen		length independent gap-penalty
matrix_file	pairscore matrix file (e.g. Dayhoff, BLOSUM etc )
use_gapdefs	set to 1 to enable the gap defaults in scanps_gapdefs.dat
                set to 0 to allow the values of ld_pen and li_pen to work.

See the full list in APPENDIX II for other valid commands.

Geoff Barton (GJB) 2002-07-23