proftmb - per-residue prediction of bacterial transmembrane beta
barrels
proftmb predicts bacterial transmembrane beta barrels from
sequence using profile fed Hidden Markov Models (HMM).
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).
- -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
Please report bugs at
<https://rostlab.org/bugzilla3/enter_bug.cgi?product=proftmb>.
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 © 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/>.