REPROF(1)							   User Commands							 REPROF(1)

NAME

       reprof - predict protein secondary structure and solvent accessibility

SYNOPSIS

       reprof -i [query.blastPsiMat] [OPTIONS]

       reprof -i [query.fasta] [OPTIONS]

       reprof -i [query.blastPsiMat|query.fasta] --mutations [mutations.txt] [OPTIONS]

DESCRIPTION

       Predict protein secondary structure and solvent accessibility.

   Output Format
       The output format is self-explanatory, i.e. the colums of the output are described in the output file itself.

OPTIONS

       -i, --input=FILE
	   Input BLAST PSSM matrix file (from Blast -Q option) or input (single) FASTA file.

       -o, --out=FILE
	   Either an output file or a directory. If not provided or a directory, the suffix of the input filename (i.e. .fasta or .blastPsiMat) is
	   replaced to create an output filename.

       --mutations=[all|FILE]
	   Either the keyword "all" to predict all possible mutations or a file containing mutations one per line such as "C12M" for C is mutated
	   to M on position 12:

	    C30Y
	    R31W
	    G48D

	   This mutation code is also attached to the output filename using "_".  An additional file ending "_ORI" contains the prediction using
	   no evolutionary information even if a BLAST PSSM matrix was provided.

       --modeldir=DIR
	   Directory where the model and feature files are stored.  Default: /usr/share/reprof.

AUTHOR

       Peter Hoenigschmid hoenigschmid@rostlab.org, Burkhard Rost

EXAMPLES

       Prediction from BLAST PSSM matrix for best results:
	    reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/example.Q.reprof

       Prediction from FASTA file:
	    reprof -i /usr/share/doc/reprof/examples/example.fasta -o /tmp/example.fasta.reprof

       Prediction from BLAST PSSM matrix file using the mutation mode:
	    reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/mutations_example.Q.reprof --mutations /usr/share/doc/reprof/examples/mutations.txt
	    # Result files for the above call are going to be:
	    # /tmp/mutations_example.Q.{reprof,reprof_F172P,reprof_M1Q,reprof_N34Y,reprof_ORI} - see --mutations for a description of the extensions.

COPYRIGHT

       This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by
       the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

       This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.

       You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>.

BUGS

       https://rostlab.org/bugzilla3/enter_bug.cgi?product=reprof

SEE ALSO

       blast2(1)

       http://rostlab.org/

1.0.1								    2012-01-13								 REPROF(1)