---
name: "reprof"
section: "1"
platform: "linux"
package: "reprof"
version: "1.0.1-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/reprof"
---

# reprof(1)

predict protein secondary structure and solvent accessibility

## 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)](/blast2/1.md)

http://rostlab.org/