06-12-2011
Hi,
sorry, I thought the longer examples help to better understand the structure, because the input files are a mess, but they are given to me like that.
I shortened the examples in my former posts. I hope now it becomes more clear what I wanna do.
Thanks a lot!
tempestas
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LEARN ABOUT DEBIAN
reprof
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)