Man page - ncoils(1)

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Manual

NCOILS(1) User Commands NCOILS(1)

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.

fasta output - coils as 'x', like '-x' in seg
concise mode - which sequences have any coils (and how many)
for concise mode - only report sequence if >= min coil segments
minimum P to define coil segment; DEFAULT = 0.5
window size; DEFAULT = 21
weight heptad positions a&d the same as b,c,e,f,g
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

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>

2021-08-15 2002