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