This file sets default gap penalty combinations for each matrix type and mode. If USE_GAPDEFS is set to 1, then scanps will take the default gap penalty combinations from the scanps_defaults.dat file for the given matrix and MODE. These values will OVERRIDE any penalties specified in the scanps_defaults.dat file, or on the command line. If you wish to specify non-default gap penalty combinations, then set USE_GAPDEFS (ugd) to 0.
For example:
If the scanps_gapdefs.dat file has the following entries:
#Format is: # mode:matrix_name:ld_pen:li_pen:fs_pen:fse_pen # 0:nmd.mat:8:0:0:0 2:nmd.mat:4:12:0:0 0:md.mat:8:0:0:0 2:md.mat:0.2:12:0:0 #
and USE_GAPDEFS = 1, then
scanps -s hahu.seq -mode 200 -m nmd.mat -bdb swissprot
will do a scan of the swissprot database with the nmd.mat matrix and a penalty of 8
scanps -s hahu.seq -mode 202 -m md.mat -bdb swissprot
would do an affine scan with the penalties of ld_pen 0.2, li_pen 12.
scanps -s hahu.seq -mode 2 -m md.mat -bdb swissprot -ugd 0 -li_pen 12 -ld_pen 4
would do the affine scan with penalties of 12, 4 rather than 12, 0.2.
WARNING: With the exception of the values for BLOSUM50 the scanps_gapdefs.dat file contains numbers that I guessed might be appropriate for the given matrix and mode. They are almost certainly not the optimum choices.