proftmb(1) 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/>.

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