PWM Files

A pwm file describes a a position weight matrix (rows are amino acids, columns are ligand positions) where each cell in the matrix represents the frequency of observing a specific amino acid at a given ligand position.

Each file consists of 21 lines with the first line containing the name of the protein. For the remaining 20 lines (one per amino acid) each line contains tab delimited fields (one field per ligand position) with each field containing the frequency of observing the amino acid at that position.

Example (for a ligand with 6 positions):

Protein A
A       0       0       1       0       4       0
C       2       0       0       0       0       0
D       0       0       0       0       0       0
E       1       0       0       0       0       0
F       2       1       1       0       0       0
G       4       1       2       1       0       0
H       0       2       3       3       0       0
I       0       0       0       1       0       0
K       0       0       2       0       0       0
L       1       1       1       0       1       15
M       1       0       0       0       0       0
N       0       2       0       0       0       0
P       0       0       0       0       5       0
Q       0       0       0       0       0       0
R       1       2       1       10      1       0
S       0       1       2       0       1       0
T       0       3       1       0       0       0
V       1       2       1       0       1       0
W       1       0       0       0       2       0
Y       1       0       0       0       0       0

Project Files

To open several pwm files at once, simply link them all in a single project file. A project file is a text file containing the absolute paths of multiple pwm files. Opening the project file in a supporting application, such as BRAIN or LOLA, will open each of the underlying pwm files in a single step, allowing multiple profiles to be processed.

Example:

#ProjectFile
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/pwmA-1.pep.txt
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/pwmA-1.pep.txt
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/pwmB-1.pep.txt
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/pwmB-2.pep.txt
/Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/pwmC-3.pep.txt

NOTE: The first line of the project file must contain the text "#ProjectFile".