PSCOILS usage

The program psCoils.py is written in python and it is distributed under the GPL License,

psCoils.py  is free software and can be redistributed  and/or 
modified under the terms of the GNU General Public License as 
published by the Free Software Foundation.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

psCoils.py incorporates both COILS and our version of PCOILS, since the original one [2] were not explicitly described. Just typing the program name psCoils.py on the standard output will appear

USAGE:  ./psCoils.py -f fasta  -p profile [options]
Options:
 -W 14/21/28 # one of the possible windows (default 21)
 -w w/uw  # weight or unweight default=uw
 -l T/F  # print prediction labels when set T (default) if P>0.5
 -L [0.0,1.0] lambda value. It will be used only if both -f and -p are set

The parameters are the standard one defined for COILS, such as:

• -W: the input window that is set to 21 as default;
• -w: can set the heptad weighted w, or unweighted uw periodicity
• -l: set the label printing in the output options (unless -l F is set)
• -L: this set the linear weighting scheme between sequence and profile, according to $\lambda$ Sequence +(1-$\lambda$) Profile.

psCoils.py can be used as COILS, PCOILS or PSCOILS depending on the different input provided, such as:

• As COILS: use only -f fasta option.
• As PCOILS: use only -p profile option.
• As PSCOILS: use both -f fasta -p profile options.

A typical output is

 Pos A Hep Score   Prob    Gcc     Gg    Pred (Loop=L Coiledcoil=C)
   1 C a   0.480   0.000   0.000   0.927 L
   2 M a   0.804   0.000   0.001   4.596 L
   3 S b   0.804   0.000   0.001   4.596 L
..

where Pos is the sequence position, A contains the residue sequence (only an x if PCOILS is used), Prob is the computed probability as described above, Gcc and Gg are Gaussian values obtained as described above and Pred is the label associated at Prob if its value is greater of $0.5$.