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