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=head1 NAME
ncoils - prediction of coiled-coil secondary structure elements
=head1 SYNOPSIS
ncoils [OPTION] < [FASTA FILE]
ncoils -f < /usr/share/doc/ncoils/1srya.fa
=head1 DESCRIPTION
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.
=head1 OPTIONS
=over
=item -f, -fasta
fasta output - coils as 'x', like '-x' in seg
=item -c
concise mode - which sequences have any coils (and how many)
=item -min_seg <int>
for concise mode - only report sequence if >= min coil segments
=item -min_P <float>
minimum P to define coil segment; DEFAULT = 0.5
=item -win <int>
window size; DEFAULT = 21
=item -w
weight heptad positions a&d the same as b,c,e,f,g
=item -v
verbose/debug mode - print extra junk
=back
=head1 EXAMPLES
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<ncoils -win 14 < /usr/share/doc/ncoils/1srya.fa>
=head1 ENVIRONMENT
COILSDIR - specifies the directory containing the file new.mat overriding the default F</usr/share/ncoils>
=head1 FILES
=over
=item F</usr/share/ncoils/*.mat>
matrix data files
=back
=head1 AUTHOR
R.B. Russell, A.N. Lupas
=head1 COPYRIGHT AND LICENSE
GPL
Based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164
=head1 SEE ALSO
L<coils-wrap(1)>, L</usr/share/doc/coils/README>, L<http://www.russelllab.org/cgi-bin/coils/coils-svr.pl>
=over
=item A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513-525, 1996
=item A. Lupas, M. Van Dyke, and J. Stock: Predicting coiled coils from protein sequences. Science, 252, 1162-1164, 1991
=back
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