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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
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