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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)

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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)
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