ncoils1

Usage

Overview

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

Copyright and license

GPL

Based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164