---
name: "proftmb"
section: "1"
platform: "linux"
package: "proftmb"
version: "1.1.12-11+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/proftmb"
---

# proftmb(1)

per-residue prediction of bacterial transmembrane beta barrels

## NAME

proftmb - per-residue prediction of bacterial transmembrane beta barrels

## SYNOPSIS

**proftmb** \[*options*\]

## DESCRIPTION

proftmb predicts bacterial transmembrane beta barrels from sequence using profile fed Hidden Markov Models (HMM).

### Output format

Self-annotating.  Letters of prediction: 'i' - inside cytoplasm, 'O' - outside cytoplasm, 'U' - up (on chain moving out of cytoplasm), 'D' - down (on chain moving into cytoplasm).

### References

- Bigelow, H. and Rost, B. (2006). PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res, 34(Web Server issue), W186-8.

  ### To invoke the menu, type:

-

  proftmb **--menu**

### The options are:

- **-d**, **--directory-root** \<STRING\>

  root path where files (options **-s**,-r,-l,-a,-e,-t,-u,-z,-n) reside

- **-a**, **--reduction-state-decode** \<STRING\>

  state reduction for decoding

- **-b**, **--reduction-state-report** \<STRING\>

  state reduction for reporting

- **-m**, **--membrane-strand-states** \<STRING\>

  list of membrane strand states

- **-z**, **--z-curve-file**

  \<STRING\>        file containing means and sd's at integral length values

- **-x**, **--z-calibration-curve** \<STRING\>

  file mapping coverage and accuracy values to z-scores

- **-n**, **--null-frequency** \<STRING\>

  background frequency file

- **-c**, **--minimum-score-cutoff** \<DOUBLE\>

  minimum z-score for per-residue prediction

- **-o**, **--outfile-prefix** \<STRING\>

  output file prefix for the three files generated: PREFIX\_dat.txt, PREFIX\_proftmb\_pretty.txt PREFIX\_proftmb\_tabular.txt

- **-s**, **--static-model-data** \<STRING\>

  data representing the model architecture

- **-t**, **--trained-params** \<STRING\>

  params representing the encoded training data

- **-q**, **--test-blastQ-file-or-dir** \<STRING\>

  psiblast profile (**-Q**) or directory (full pathname or relative to current directory) with many profiles

- **-w**, **--single-sequence-name** \<STRING\>

  if **-q** option points to a single file, this is the name

- **-v**, **--list-blastQ-files** \<STRING\>

  list of psiblast files to process in directory (leave blank to process all files)

- **--outfile-pretty** \<STRING\>

  pretty output file (overrides automatic name PREFIX\_proftmb\_pretty.txt)

- **--outfile-tab**

  \<STRING\>        tabulated output file (overrides automatic name PREFIX\_proftmb\_tabular.txt)

- **--outfile-dat**

  \<STRING\>        data output file (overrides automatic name PREFIX\_dat.txt)

- **--version**

  \<BOOL\>          output version information and exit

- **--quiet**

  \<BOOL\>          be quiet

## BUGS

Please report bugs at \<https://rostlab.org/bugzilla3/enter\_bug.cgi?product=proftmb\>.

## EXAMPLES

```
 proftmb @/usr/share/proftmb/options -q /usr/share/doc/proftmb/examples/example.Q -o /tmp/example
```

The above produces 3 output files: */tmp/example\_proftmb\_tabular.txt*, */tmp/example\_proftmb\_pretty.txt* and */tmp/example\_dat.txt*.  Compare these to the examples in */usr/share/doc/proftmb/examples*.

## COPYRIGHT

Copyright © 2004 Henry Bigelow

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 package 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/\>.