NAME 

   RepeatFinder - search for statistically significant, high-complexity 
		  aminoacid repeats.

SYNOPSIS 

   RepeatFinder -f filename [-b] [-d] [-e] [-s] [-g] [-j] [-r] [-l] [-t] 

DESCRIPTION

   RepeatFinder is an ancillary program designed to automatize the use the
   Gibbs  sampler  program (Neuwald et al.,  1995)  for  the  detection of
   statistically significant, ungapped aminoacid repeats. Input  sequences
   need to  be in fasta  format. Detected repeats  are stored  in the file 
   'result'.   RepeatFinder  runs  the  Gibbs  sampler  program  -g  times
   searching  for  repeated  modules  ranging  in  size between -b  and -e 
   aminoacids, using an increment step of -s aminoacids. Only modules with
   a significance  below  -t  threshold  are  considered  as  significant. 
   p-value of the alignment is calculated according to the Karlin-Altschul
   statistic  (Karlin and Altschul, 1993).  Sequences need to be of length
   at least  -l aminoacids in order to be  analyzed. The option -j  allows
   to  just  count  the  input  sequences.  The option -r can  be  used to
   restart the program after a computer crash without losing what has been
   already  calculated.  Parameters to  be  passed  to  the  Gibbs sampler
   program are enclosed in the file 'gibbspar'.

OPTIONS

   -b	smallest size of the repeated modules       (default: 5)

   -e	biggest size of the repeated modules        (default: 30)

   -s	increment step between -b and -e parameters (default: 5)

   -g	# runs of the Gibbs sampler                 (default: 50)

   -r   restart from a previous crash               (default: off)

   -l	minimum sequence length                     (default: 100)

   -t	significance threshold (p-value)            (default: 0.001)

   -d 	max number of diagonals in the block        (default: 50)


EXAMPLE

   The following example:

	RepeatFinder -f prion.tfa -b 10 -e 20 -t 0.0005

   will prompt RepeatFinder to run the Gibbs sampler to detect repeats (if
   any) in the  sequence 'prion.tfa'. It  will search for  repeats ranging
   between 10  and  20  aminoacids  and  will  report  only  those  with a 
   significance (p-value) below 0.0005.



REFERENCES

   Karlin S,  Altschul SF.   Applications  and  statistics  for  multiple
   high-scoring segments in molecular sequences. Proc Natl Acad Sci U S A
   1993 Jun 15;90(12):5873-7

   Neuwald AF,  Liu JS,  Lawrence CE.  Gibbs motif sampling:  detection of
   bacterial outer  membrane  protein  repeats. Protein Sci 1995 Aug;4(8):
   1618-32.

   Lavorgna G,  Patthy L,  Boncinelli E.  Were  protein  internal  repeats 
   formed by 'bricolage'? Trends Genet. 17, 120-123 (2001).


README
Uncompress RepeatFinder2_02.tar.Z by typing "uncompress
RepeatFinder2_02.tar.Z". Then, extract the files by typing "tar -xvf
RepeatFinder2_02.tar". This will create a directory "RepeatFinder2_02",
which contains three subdirectories named "code", "doc" and "data". To
compile switch to the 'code' directory and type "./compile" on the command
line.  (You may need to reset the CC macro in code/makefile to correspond
to your compiler; the default is CC = cc). This will create 6 executable
files in the current directory: xnu, gibbs, RepeatFinder,
prosperolauncher, panalyzer and rfanalyzer. The gibbs program corresponds
to a slighlty modified (i.e., less verbose) version of the gibbs sampler 
program by Andy Neuwald et al.  The xnu software by Claverie and Slates
was used to filter out low-complexity repeats from the protein sequence
sets, when using the prospero program.
RepeatFinder and prosperolauncher are two ancillary programs which use,
respectively, the gibbs sampler and the prospero programs,
in order to possibly detect statistically significant repeats from a
sequence set of proteis in fasta format. rfanalyzer and panalyzer programs
 are used for analyzing the output generated, respectively, by the
programs RepeatFinder and Prospero. Please refer to the doc section for
details on program usage.
References

        Neuwald  A.F.,   Liu J.S.,   Lawrence C.E.  (1995) Gibbs motif
        sampling of bacterial outer membrane protein  repeats. Protein
        Sci 4, 1618-32. (gibbs sampler)

        Lavorgna G.,  Patthy, L.,  Boncinelli E. (2001)  Were  protein
        internal  repeats  formed  by  'bricolage'?  Trends  Genet 17,
        120-3. (RepeatFinder)

        Claverie, J.M. & States, D.J. (1993).  Information  enhancement  
	methods  for  large  scale  sequence  analysis.  Computers  and
	Chemistry 17, 191-201. (xnu program)

	Mott, R. 2000  Accurate  Formula for  P-values  of gapped local
	sequence  and  profile  alignments.  J. Mol. Biol  300:649-659. 
	(Prospero program)