File: README

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pftools 3+dfsg-3
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"pftools" is a collection of experimental programs supporting the
generalized profile format and search method of PROSITE.
A description of the generalized profile format is given in file:

   profile.txt

Version 2.2 contains FORTRAN 77 source code and manual pages for
the following programs:

   pfsearch
   pfscan
   psa2msa
   gtop  
   htop
   ptoh
   pfmake
   pfw
   pfscale 
   ptof
   6ft
   2ft

These programs have successfully been compiled and tested under
Solaris, IRIX64, HP-UX, and Linux operating systems, using
the GNU g77 compiler. 

For compilation with native f77 compilers, the Makefile needs
to be modified according to instructions given therein.  

For use under HP-UX, the file sterr.f should also be modified
according to instructions given therein. 

To run the programs on machines with less than 32 MB RAM, modify 
the file ardim.f according to instructions given therein. 

The "Integer*2" declarations may cause problems with early versions
of the g77 compiler; solution: replace "Integer*2" by "Integer". 

In order to compile the programs, type:

   make

This will create the nine binaries listed above. To install the 
the binaries and the corresponding manual pages, first define
the target directories in the Makefile, then type:

   make install

*-----
 
Further included in this release are the following demo data files:

   CVPBR322
   sh3.seq 
   GTPA_HUMAN
   sh3.msf
   ecp.prf
   sh3.gpr
   sh3.prf 
   pfam_sh3.hmm
   prosite13.prf
   standard.random
   blosum45.cmp
   score.lis
   coils.prf
   MYSA_HUMAN
   R76849.seq

plus the following additional substution matrices in old GCG format: 

   blosum30.cmp
   blosum50.cmp
   blosum62.cmp
   blosum65.cmp
   blosum80.cmp
   blosum100.cmp
   gonnet.cmp
   pam30.cmp
   pam40.cmp
   pam80.cmp
   pam120.cmp
   pam160.cmp
   pam200.cmp
   pam220.cmp
   pam250.cmp
   pam400.cmp

a test script: 

   test.sh 

and a test ouput file: 

   test.out

To test the programs, type: 

   sh  test.sh > out 
   diff test.out out 

Some rounding or formatting variation may occur with real number
editing. With g77 there will be lots of small integer rounding
differences in the result of test 7.  

Note that the file pfam_sh3.hmm contains a hidden Markov model from the
PFAM A collection release 4.0 (see http://www.sanger.ac.uk/Pfam).

*-----

Total number of files included in this directory: 101

*-----

Please send bug reports to:

   Philipp Bucher
   E-mail: Philipp.Bucher@isrec.unil.ch

Philipp Bucher, July 1999