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.
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/