prdf [-fghks] - interactive mode
prdf also allows a more sophisticated shuffling method: residues can be shuffled within a local window, so that the order of residues 1-10, 11-20, etc, is destroyed but a residue in the first 10 is never swapped with a residue outside the first ten, and so on for each local window.
(1) prdf -w 10 musplfm.aa lcbo.aa 1 250
Compare the amino acid sequence in the file musplfm.aa with that in lcbo.aa, then shuffle lcbo.aa 250 times using a local shuffle with a window of 10 and calculate initial and optimized similarity scores using Ktup = 1. Report the significance of the unshuffled musplfm/lcbo comparison scores with respect to the shuffled scores.
(2) prdf musplfm.aa lcbo.aa 2
Compare the amino acid sequence in the file musplfm.aa with the sequences in the file lcbo.aa using ktup = 2.
(3) prdf
Run prdf in interactive mode. The program will prompt for the file name of the two query sequence files, the ktup, and the number of shuffles to be used. 100 shuffles are calculated by default; 250 - 500 shuffles should provide more accurate probability estimates.
prss can be directed to change the scoring matrix, gap penalties, and shuffle parameters by entering options on the command line (preceeded by a `-'). All of the options should preceed the file names number of shuffles.
-f # Penalty for the first residue in a gap (-12 by default).
-g # Penalty for additional residues in a gap (-2 by default).
-h Do not display histogram of similarity scores.
-k # (GAPCUT) Sets the threshold for joining the initial regions for calculating the initn score.
-Q -q
"quiet" - do not prompt for filename.
-O filename
send copy of results to "filename."
-s str
(SMATRIX) the filename of an alternative scoring matrix file. For
protein sequences, BLOSUM50 is used by default; PAM250 can be used
with the command line option -s 250(or with -s pam250.mat).
The curve fitting routines in rweibull.c were provided by Phil Green, Washington U., St. Louis.