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/