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/>.

proftmb 1.1.12                                    January 2022                                        PROFTMB(1)