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Manual Reference Pages  -  PRDF (1)


prdf - test a protein sequence similarity for significance




prdf [-f # -g # -h -k # -O filename -s SMATRIX -w window-size ] sequence-file-1 sequence-file-2 [ ktup ] [ #-of-shuffles ]

prdf [-fghks] - interactive mode


prdf is used to evaluate the significance of a protein sequence similarity score by comparing two sequences and calculating initial and optimized similarity scores, and then repeatedly shuffling the second sequence, and calculating the initial and optimized scores. Extreme value distributions are then fit to each of the three distributions of scores. The characteristic parameters of the extreme value distribution are then used to estimate the probability that each of the unshuffled sequence scores would be obtained by chance in one sequence, or in a number of sequences equal to the number of shuffles. This program is derived from rdf2, which was described by Pearson and Lipman, PNAS (1988) 85:2444-2448, and Pearson (Meth. Enz. 183:63-98). Use of the extreme value distribution for estimating the probabilities of similarity scores was described by Altshul and Karlin, PNAS (1990) 87:2264-2268. The ’z-values’ calculated by rdf2 are not as informative as the P-values and expectations calculated by prdf.

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).




Bill Pearson

The curve fitting routines in rweibull.c were provided by Phil Green, Washington U., St. Louis.

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