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PRSS3(1)		     General Commands Manual			PRSS3(1)

NAME
     prss - test a protein sequence similarity for significance

SYNOPSIS
     prss34  [-Q  -A  -f  # -g # -H -O file -s SMATRIX -w # -Z # -k # -v # ] se-
     quence-file-1 sequence-file-2 [ #-of-shuffles ]

     prfx34 [-Q -A -f # -g # -H -O file -s SMATRIX -w # -z 1,3 -Z # -k # -v #  ]
     sequence-file-1 sequence-file-2 [ ktup ] [ #-of-shuffles ]

     prss34(_t)/prfx34(_t) [-AfghksvwzZ] - interactive mode

DESCRIPTION
     prss34  and  prfx34 are used to evaluate the significance of a protein:pro-
     tein, DNA:DNA ( prss34 ), or translated-DNA:protein  (  prfx34  )	sequence
     similarity  score	by comparing two sequences and calculating optimal simi-
     larity scores, and then repeatedly shuffling the second sequence, and  cal-
     culating  optimal	similarity scores using the Smith-Waterman algorithm. An
     extreme value distribution is then fit  to  the  shuffled-sequence  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 se-
     quences equal to the number of shuffles.	This  program  is  derived  from
     rdf2,  described by Pearson and Lipman, PNAS (1988) 85:2444-2448, and Pear-
     son (Meth. Enz.  183:63-98).  Use of the extreme value distribution for es-
     timating the probabilities of similarity scores was  described  by  Altshul
     and  Karlin,  PNAS (1990) 87:2264-2268.  The and expectations calculated by
     prdf.  prss34 calculates optimal scores using the same  rigorous  Smith-Wa-
     terman  algorithm	(Smith	and  Waterman, J. Mol. Biol. (1983) 147:195-197)
     used by the ssearch34 program.  prfx34 calculates scores  using  the  FASTX
     algorithm (Pearson et al. (1997) Genomics 46:24-36.

     prss34  and  prfx34  also	allow  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  lo-
     cal window.

EXAMPLES
     (1)    prss34  -v 10 musplfm.aa lcbo.aa

     Compare  the  amino  acid	sequence  in  the  file  musplfm.aa with that in
     lcbo.aa, then shuffle lcbo.aa 200 times using a local shuffle with a window
     of 10.  Report the significance of the unshuffled	musplfm/lcbo  comparison
     scores with respect to the shuffled scores.

     (2)    prss34 musplfm.aa lcbo.aa 1000

     Compare  the  amino acid sequence in the file musplfm.aa with the sequences
     in the file lcbo.aa, shuffling lcbo.aa 1000 times.  Shuffles  can	also  be
     specified with the -k # option.

     (3)    prfx34 mgstm1.esq xurt8c.aa 2 1000

     Translate	the  DNA  sequence  in the mgstm1.esq file in all six frames and
     compare it to the amino acid sequence in the file xurt8c.aa,  using  ktup=2
     and  shuffling  xurt8c.aa	1000  times.  Each comparison considers the best
     forward or reverse alignment with frameshifts, using  the	fastx  algorithm
     (Pearson et al (1997) Genomics 46:24-36).

     (4)    prss34/prfx34

     Run prss in interactive mode.  The program will prompt for the file name of
     the two query sequence files and the number of shuffles to be used.

OPTIONS
     prss34/prfx34  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 shuf-
     fles.

     -A     Show unshuffled alignment.

     -f #   Penalty for opening a gap (-10 by default for proteins).

     -g #   Penalty  for  additional  residues in a gap (-2 by default) for pro-
	    teins.

     -H     Do not display histogram of similarity scores.

     -k #   Number of shuffles (200 is the default)

     -Q -q  "quiet" - do not prompt for filename.

     -O filename
	    send copy of results to "filename."

     -s str
	    specify the scoring matrix.  BLOSUM50 is used by  default  for  pro-
	    teins;  +5/-4 is used by defaul for DNA.  prss34 recognizes the same
	    scoring matrices as fasta34, ssearch34,  fastx34,  etc;  e.g.  BL50,
	    P250,  BL62, BL80, MD10, MD20, and other matrices in BLAST1.4 matrix
	    format.

     -v #   Use a local window shuffle with a window size of #.

     -z #   Calculate statistical significance using the mean/variance (moments)
	    approach used by fasta34/ssearch or from  maximum  likelihood  esti-
	    mates of lambda and K.

     -Z #   Present statistical significance as if a '#' entry database had been
	    searched  (e.g.  "-Z  50000" presents statistical significance as if
	    50,000 sequences had been compared).

ENVIRONMENT VARIABLES
     (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 P250(or with -s pam250.mat).  BLOSUM62 (-s BL62) and PAM120
     (-S P120).

SEE ALSO
     ssearch3(1), fasta3(1).

AUTHOR
     Bill Pearson
     wrp@virginia.EDU

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