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README.pftools.v2.3.md

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Description of pftools release 2.3 package and files

Contents:

  1. Package description
  • Profile format
  • Programs and manual pages
  • Compilation issues
  1. Installation
  • Compiling
  • Installing
  1. File list
  2. Testing
  3. Contact

Package description

The pftools package 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 the file:

doc/profile.txt

The official web site for the pftools package can be found under:

pftools

Further information on PROSITE specific applications of the pftools programs can be found at the following URL:

PROSITE

Release 2.3 contains FORTRAN 77 source code and manual pages for the following programs:

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

Some supplementary manual pages describing the psa and xpsa file formats have also been included.

These programs have successfully been compiled and tested under Solaris, IRIX64, HP-UX, Tru64 and Linux operating systems, using the GNU g77 or f77 compilers.

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.

The buffer sizes in release 2.3 of the pftools have been significantly increased to handle large sequences and profiles. Therefore it might be necessary to reduce the buffer sizes in order to run the programs on machines with less RAM. This can be achieved by modifying the file ardim.f according to instructions given therein.

The "Integer2" declarations may cause problems with early versions of the g77 compiler; solution: replace "Integer2" by "Integer".

Installation

The compressed tar archive can be extracted to the current directory using the following command:

   tar -xzvf pft2.3.tar.gz

This will create a directory containing the source and package files.

In order to compile the programs on Unix like systems with a FORTRAN 77 compiler, change into the source directory and simply type:

   make all

This will create the 12 binaries listed above. To install the binaries and the corresponding manual pages, an installation script has been provided. It can be invoked using:

   make install

The installation script will ask the user the destination directory for the pftools package. This directory will contain all the supplementary files, as well as a bin directory for the executable programs. The installer will then create symbolic links to the binary programs in a directory specified by the user. This directory should be included in the users PATH variable for him to be able to execute the pftools programs. In a last step, the installer will link the man pages in the system wide man page location, this location can also be specified by the user. After successful installation, the build directory can safely be deleted.

Note that you should have write permissions on the destination directories specified during installation. For system wide installation you may need root privileges, if necessary contact your system administrator.

File list

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

Testing

A test script is provided. It will simply execute all the pftools binaries with some example files. The test script test.sh should be executed in the same directory as the binaries and the demo files. An example test output file test.out is provided as a reference. To test the programs, type:

   ./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 Pfam).

Contact

Please send bug reports to:

[email protected]

The pftools package was originaly developed by Philipp Bucher and was maintained by Thierry Schuepbach at the:

SIB Swiss Institute of Bioinformatics
Vital-IT Group
Quartier Sorge, Batiment Amphipole
CH-1015 Lausanne
Switzerland

SIB