NAME

       ncoils - prediction of coiled-coil secondary structure elements

SYNOPSIS

       ncoils [OPTION] < [FASTA FILE]

       ncoils -f < /usr/share/doc/ncoils/1srya.fa

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.

OPTIONS

       -f, -fasta
           fasta output - coils as 'x', like '-x' in seg

       -c  concise mode - which sequences have any coils (and how many)

       -min_seg <int>
           for concise mode - only report sequence if >= min coil segments

       -min_P <float>
           minimum P to define coil segment; DEFAULT = 0.5

       -win <int>
           window size; DEFAULT = 21

       -w  weight heptad positions a&d the same as b,c,e,f,g

       -v  verbose/debug mode - print extra junk

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"

ENVIRONMENT

       COILSDIR - specifies the directory containing the file new.mat overriding the default
       /usr/share/ncoils

FILES

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

AUTHOR

       R.B. Russell, A.N. Lupas

COPYRIGHT AND LICENSE

       GPL

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

SEE ALSO

       coils-wrap(1), "usr/share/doc/coils/README",
       <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