SYNOPSISncoils [OPTION] < [FASTA FILE]
ncoils -f < /usr/share/doc/ncoils/1srya.fa
DESCRIPTIONncoils 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.
- -f, -fasta
- fasta output - coils as 'x', like '-x' in seg
- 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
- weight heptad positions a&d the same as b,c,e,f,g
- 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"
ENVIRONMENTCOILSDIR - specifies the directory containing the file new.mat overriding the default /usr/share/ncoils
- matrix data files
AUTHORR.B. Russell, A.N. Lupas
COPYRIGHT AND LICENSEGPL
Based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164