charge

Function

Description

charge reads a protein sequence and writes a file (or plots a graph) of the mean charge 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 a datafile (Eamino.dat) of amino acid properties. 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 the window, which by default is 5 residues.

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