charge
Function
Description
charge reads a protein sequence and writes a file (or plots a
graph) of the charges of the amino acids within a window of specified
length as the window is moved along the sequence.
Algorithm
charge uses the column "charge" from the datafile
Eamino.dat. It gives the residues 'D' and 'E' a charge of -1,
'K' and 'R' a charge of +1, and the residue 'H' a charge of +0.5. Then
it calculates the mean charge across -window (default is 5).
Usage
Command line arguments
Input file format
charge reads in a protein sequence.
Output file format
If the option '-plot' is specified then charge displays a graph
of the charge along the sequence otherwise it writes out a file
containing the charges within a window starting at each position along
the sequence.
The output file contains two columns separated by space or TAB
characters. The first column is the position of the start of the
window. The second column is the charge of the amino acids within that
window.
Data files
charge reads the data file 'Eamino.dat' to find the charge of
the amino acids in the protein.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
Author(s)
History
Target users
Comments