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.\" ========================================================================
.\"
.IX Title "COILS-WRAP 1"
.TH COILS-WRAP 1 "2021-08-15" "2002" "User Commands"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
coils\-wrap \- runs ncoils three times to give you a three\-window output
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
coils-wrap [\s-1OPTION\s0]
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
coils-wrap runs ncoils three times to give you a three-window output.
.PP
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.
.SH "OPTIONS"
.IX Header "OPTIONS"
.IP "\-i" 4
.IX Item "-i"
input file in \s-1FASTA\s0 format
.IP "\-o" 4
.IX Item "-o"
output file
.IP "\-r" 4
.IX Item "-r"
raw output file, default: `<output file>_raw'
.IP "\-m" 4
.IX Item "-m"
matrix type; set matrix (\s-1MTK\s0 or \s-1MTIDK\s0)
.IP "\-w" 4
.IX Item "-w"
weight a&d = b,c,e,f&g (boolean)
.SH "EXAMPLES"
.IX Header "EXAMPLES"
\&\f(CW\*(C`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\*(C'\fR
.PP
\&\f(CW\*(C`ncoils \-win 14 < /usr/share/doc/ncoils/1srya.fa\*(C'\fR
.SH "FILES"
.IX Header "FILES"
.IP "\fI/usr/share/coiledcoils/*.mat\fR" 4
.IX Item "/usr/share/coiledcoils/*.mat"
matrix data files
.SH "AUTHOR"
.IX Header "AUTHOR"
R.B. Russell, A.N. Lupas, 1999
.SH "COPYRIGHT AND LICENSE"
.IX Header "COPYRIGHT AND LICENSE"
\&\s-1GPL\s0
.PP
Based on Lupas, Van Dyck & Stock (1991) Science 252,1162\-1164
.SH "SEE ALSO"
.IX Header "SEE ALSO"
\&\fBncoils\fR\|(1), \*(L"usr/share/doc/coils/README\*(R", <http://www.russelllab.org/cgi\-bin/coils/coils\-svr.pl>
.IP "A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513\-525, 1996" 4
.IX Item "A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513-525, 1996"
.PD 0
.IP "A. Lupas, M. Van Dyke, and J. Stock: Predicting coiled coils from protein sequences. Science, 252, 1162\-1164, 1991" 4
.IX Item "A. Lupas, M. Van Dyke, and J. Stock: Predicting coiled coils from protein sequences. Science, 252, 1162-1164, 1991"