coils-wrap(1) [debian man page]

COILS-WRAP(1)							   User Commands						     COILS-WRAP(1)

NAME

       coils-wrap - runs ncoils three times to give you a three-window output

SYNOPSIS

       coils-wrap [OPTION]

DESCRIPTION

       coils-wrap runs ncoils three times to give you a three-window output.

       ncoils is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By
       comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that
       the sequence will adopt a coiled-coil conformation.

OPTIONS

       -i  input file in FASTA format

       -o  output file

       -r  raw output file, default: `<output file>_raw'

       -m  matrix type; set matrix (MTK or MTIDK)

       -w  weight a&d = b,c,e,f&g (boolean)

EXAMPLES

       "coils-wrap -m MTIDK -i /usr/share/doc/ncoils/1srya.fa -o /tmp/coils.out -r /tmp/coils_raw.txt && less /tmp/coils.out /tmp/coils_raw.txt"

       "ncoils -win 14 < /usr/share/doc/ncoils/1srya.fa"

FILES

       /usr/share/coiledcoils/*.mat
	   matrix data files

AUTHOR

       R.B. Russell, A.N. Lupas, 1999

COPYRIGHT AND LICENSE

       GPL

       Based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164

SEE ALSO

       ncoils(1), "usr/share/doc/coils/README", http://www.russelllab.org/cgi-bin/coils/coils-svr.pl <http://www.russelllab.org/cgi-
       bin/coils/coils-svr.pl>

       A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513-525, 1996
       A. Lupas, M. Van Dyke, and J. Stock: Predicting coiled coils from protein sequences. Science, 252, 1162-1164, 1991

2002								    2011-10-29							     COILS-WRAP(1)

PROFTMB(1)							   User Commands							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

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 (C) 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 MER-
       CHANTABILITY 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 1.1.10							   February 2012							PROFTMB(1)