Provided by: ncoils_2002-4_amd64
ncoils - prediction of coiled-coil secondary structure elements
ncoils [OPTION] < [FASTA FILE] ncoils -f < /usr/share/doc/ncoils/1srya.fa
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.
-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
"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"
COILSDIR - specifies the directory containing the file new.mat overriding the default /usr/share/ncoils
/usr/share/ncoils/*.mat matrix data files
R.B. Russell, A.N. Lupas
COPYRIGHT AND LICENSE
GPL Based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164
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