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

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/>.