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).
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.
- 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
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.
BUGS¶
Please report bugs at
<
https://rostlab.org/bugzilla3/enter_bug.cgi?product=proftmb>.
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/>.