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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

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