NAME

coils-wrap - runs ncoils three times to give you a three-window output

SYNOPSIS

coils-wrap [OPTION]

DESCRIPTION

coils-wrap runs ncoils three times to give you a three-window output.

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

-i

input file in FASTA format

-o

output file

-r

raw output file, default: `<output file>_raw'

-m

matrix type; set matrix (MTK or MTIDK)

-w

weight a&d = b,c,e,f&g (boolean)

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"

FILES

/usr/share/coiledcoils/*.mat

matrix data files

AUTHOR

R.B. Russell, A.N. Lupas, 1999

COPYRIGHT AND LICENSE

GPL

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

SEE ALSO

ncoils(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