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.