.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH PROFTMB "1" "October 2018" "proftmb 1.1.12" "User Commands"
.SH NAME
proftmb \- per-residue prediction of bacterial transmembrane beta barrels
.SH SYNOPSIS
.B proftmb
[\fI\,options\/\fR]
.SH DESCRIPTION
proftmb predicts bacterial transmembrane beta barrels from sequence using profile fed Hidden Markov Models (HMM).
.SS "Output format"
.IX Subsection "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).
.PP

.SS "References"
.IX Subsection "References"
.IP "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." 4
.IX Item "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."
.SS "To invoke the menu, type:"
.IP
proftmb \fB\-\-menu\fR
.SS "The options are:"
.TP
\fB\-d\fR, \fB\-\-directory\-root\fR <STRING>
root path where files (options
\fB\-s\fR,\-r,\-l,\-a,\-e,\-t,\-u,\-z,\-n) reside
.TP
\fB\-a\fR, \fB\-\-reduction\-state\-decode\fR <STRING>
state reduction for decoding
.TP
\fB\-b\fR, \fB\-\-reduction\-state\-report\fR <STRING>
state reduction for reporting
.TP
\fB\-m\fR, \fB\-\-membrane\-strand\-states\fR <STRING>
list of membrane strand states
.TP
\fB\-z\fR, \fB\-\-z\-curve\-file\fR
<STRING>        file containing means and sd's at integral
length values
.TP
\fB\-x\fR, \fB\-\-z\-calibration\-curve\fR <STRING>
file mapping coverage and accuracy values
to z\-scores
.TP
\fB\-n\fR, \fB\-\-null\-frequency\fR <STRING>
background frequency file
.TP
\fB\-c\fR, \fB\-\-minimum\-score\-cutoff\fR <DOUBLE>
minimum z\-score for per\-residue prediction
.TP
\fB\-o\fR, \fB\-\-outfile\-prefix\fR <STRING>
output file prefix for the three files
generated: PREFIX_dat.txt,
PREFIX_proftmb_pretty.txt
PREFIX_proftmb_tabular.txt
.TP
\fB\-s\fR, \fB\-\-static\-model\-data\fR <STRING>
data representing the model architecture
.TP
\fB\-t\fR, \fB\-\-trained\-params\fR <STRING>
params representing the encoded training
data
.TP
\fB\-q\fR, \fB\-\-test\-blastQ\-file\-or\-dir\fR <STRING>
psiblast profile (\fB\-Q\fR) or directory (full
pathname or relative to current directory)
with many profiles
.TP
\fB\-w\fR, \fB\-\-single\-sequence\-name\fR <STRING>
if \fB\-q\fR option points to a single file, this
is the name
.TP
\fB\-v\fR, \fB\-\-list\-blastQ\-files\fR <STRING>
list of psiblast files to process in
directory (leave blank to process all
files)
.TP
\fB\-\-outfile\-pretty\fR <STRING>
pretty output file (overrides automatic
name PREFIX_proftmb_pretty.txt)
.TP
\fB\-\-outfile\-tab\fR
<STRING>        tabulated output file (overrides automatic
name PREFIX_proftmb_tabular.txt)
.TP
\fB\-\-outfile\-dat\fR
<STRING>        data output file (overrides automatic name
PREFIX_dat.txt)
.TP
\fB\-\-version\fR
<BOOL>          output version information and exit
.TP
\fB\-\-quiet\fR
<BOOL>          be quiet
.SH BUGS
Please report bugs at <https://rostlab.org/bugzilla3/enter_bug.cgi?product=proftmb>.
.SH EXAMPLES
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.Vb 1
\& proftmb @/usr/share/proftmb/options \-q /usr/share/doc/proftmb/examples/example.Q \-o /tmp/example
.Ve
.PP
The above produces 3 output files: \fI/tmp/example_proftmb_tabular.txt\fR, \fI/tmp/example_proftmb_pretty.txt\fR and \fI/tmp/example_dat.txt\fR.  Compare these to the examples in \fI/usr/share/doc/proftmb/examples\fR.
.SH COPYRIGHT
Copyright \(co 2004 Henry Bigelow
.PP
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.
.PP
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.
.PP
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.