debian man page for ncoils

NCOILS(1)							   User Commands							 NCOILS(1)

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 <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								 NCOILS(1)