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ncoils - Online in the Cloud

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This is the command ncoils that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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