proftmb(1)
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/>.
Opportunity
Personal Opportunity - Free software gives you access to billions of dollars of software at no cost. Use this software for your business, personal use or to develop a profitable skill. Access to source code provides access to a level of capabilities/information that companies protect though copyrights. Open source is a core component of the Internet and it is available to you. Leverage the billions of dollars in resources and capabilities to build a career, establish a business or change the world. The potential is endless for those who understand the opportunity.
Business Opportunity - Goldman Sachs, IBM and countless large corporations are leveraging open source to reduce costs, develop products and increase their bottom lines. Learn what these companies know about open source and how open source can give you the advantage.
Free Software
Free Software provides computer programs and capabilities at no cost but more importantly, it provides the freedom to run, edit, contribute to, and share the software. The importance of free software is a matter of access, not price. Software at no cost is a benefit but ownership rights to the software and source code is far more significant.
Free Office Software - The Libre Office suite provides top desktop productivity tools for free. This includes, a word processor, spreadsheet, presentation engine, drawing and flowcharting, database and math applications. Libre Office is available for Linux or Windows.
Free Books
The Free Books Library is a collection of thousands of the most popular public domain books in an online readable format. The collection includes great classical literature and more recent works where the U.S. copyright has expired. These books are yours to read and use without restrictions.
Source Code - Want to change a program or know how it works? Open Source provides the source code for its programs so that anyone can use, modify or learn how to write those programs themselves. Visit the GNU source code repositories to download the source.
Education
Study at Harvard, Stanford or MIT - Open edX provides free online courses from Harvard, MIT, Columbia, UC Berkeley and other top Universities. Hundreds of courses for almost all major subjects and course levels. Open edx also offers some paid courses and selected certifications.
Linux Manual Pages - A man or manual page is a form of software documentation found on Linux/Unix operating systems. Topics covered include computer programs (including library and system calls), formal standards and conventions, and even abstract concepts.
