Typing ``scanps'' with no options will show you the following screen:
Options:
DATABASE SCANNING:
-s<file.seq> Query sequence file in PIR format [e.g. -shahu.seq]
-b<file.blc> Query multiple alignment in AMPS format [e.g. -bmyo.blc]
-d Read the database from standard input
-F<file.fit> File of length dependent fit parameters [e.g. -Ffits.dat]
-F1 Turn on length dependent parameters defined in
SCANPSDEFAULTS file
-g<Prob> Set probability threshold (for use with -F [e.g. -g0.001]
-n Work silently - do not show alignments
-m<file.mat> Define pair score matrix file (e.g. PAM250)
-p<N> Define gap penalty e.g. -p8
-a<N> Define mode: -a0 for top score only
-a1 for all local alignments
-c<N> Define cutoff score. [e.g. -c80]
-l<N> Define alignment length cutoff (only valid for -a1)
-o<file.seq> Define output file for sequence alignment fragments
These can then be multiply aligned later using AMPS
-V<file.gap> Define a file of variable gap penalties
-G Turn on variable gap penalties if no -V
-L<file.lk> Read the look up table file
-D<file.lk> Print out the look up table and variable gap penalties
PAIRWISE COMPARISONS:
-t<file.sec> Secondary structure file in PIR format [e.g. -thahu.sec]
-T File defined with -t is not true sec struc.
-E Only consider the top scoring alignment in pairwise mode
-Y Do all pairs output down to threshold defined by -g
-y Do all pairs output down to threshold defined by -g
Also output start and end residues of each aligment.
-X Produce output in a format suitable for program oc
Hopefully, most of this is self explanatory. The options that are not discussed in the previous sections are:
-o When -a1 is set, this outputs the aligned fragments from the database file to the defined file in .seq file format.
-V, -G -L and -D Allow variable gap-penalties and user-defined per-residue scoring schemes to be applied when scanning with a sequence or an alignment. I will document and describe these features in the next release.