reprof (1)

reprof -i [query.blastPsiMat] [\s-1OPTIONS\s0]

reprof -i [query.fasta] [\s-1OPTIONS\s0]

reprof -i [query.blastPsiMat|query.fasta] --mutations [mutations.txt] [\s-1OPTIONS\s0]

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.

-i, --input=\s-1FILE\s0

Input \s-1BLAST\s0 \s-1PSSM\s0 matrix file (from Blast -Q option) or input (single) \s-1FASTA\s0 file.

-o, --out=\s-1FILE\s0

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 \*(L"all\*(R" to predict all possible mutations or a file containing mutations one per line such as \*(L"C12M\*(R" for C is mutated to M on position 12:

 C30Y
 R31W
 G48D

This mutation code is also attached to the output filename using \*(L"_\*(R". An additional file ending \*(L"_ORI\*(R" contains the prediction using no evolutionary information even if a \s-1BLAST\s0 \s-1PSSM\s0 matrix was provided.

--modeldir=\s-1DIR\s0

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

Peter Hoenigschmid [email protected], Burkhard Rost

Prediction from \s-1BLAST\s0 \s-1PSSM\s0 matrix for best results:

reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/example.Q.reprof

Prediction from \s-1FASTA\s0 file:

reprof -i /usr/share/doc/reprof/examples/example.fasta -o /tmp/example.fasta.reprof

Prediction from \s-1BLAST\s0 \s-1PSSM\s0 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.

This program is free software: you can redistribute it and/or modify it under the terms of the \s-1GNU\s0 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 \s-1WITHOUT\s0 \s-1ANY\s0 \s-1WARRANTY\s0; without even the implied warranty of \s-1MERCHANTABILITY\s0 or \s-1FITNESS\s0 \s-1FOR\s0 A \s-1PARTICULAR\s0 \s-1PURPOSE\s0. See the \s-1GNU\s0 General Public License for more details.

You should have received a copy of the \s-1GNU\s0 General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

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

blast2\|(1)

http://rostlab.org/