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