
                               EMBOSS: charge
     _________________________________________________________________
   
                                Program charge
                                       
Function

   Protein charge plot
   
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.
   
Usage

   Here is a sample session with charge:
   
% charge sw:hbb_human
Protein charge plot
Output file [hbb_human.charge]:

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-seqall]            seqall     Sequence database USA
*  -graph              xygraph    Graph type
*  -outfile            outfile    Output file name

   Optional qualifiers:
   -window             integer    Window

   Advanced qualifiers:
   -aadata             string     Amino acid property data file name
   -plot               bool       Produce graphic

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-seqall]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   -graph Graph type EMBOSS has a list of known devices, including
   postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows,
   x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm,
   png EMBOSS_GRAPHICS value, or x11
   -outfile Output file name Output file <sequence>.charge
   Optional qualifiers Allowed values Default
   -window Window Integer 1 or more 5
   Advanced qualifiers Allowed values Default
   -aadata Amino acid property data file name Any string is accepted
   Eamino.dat
   -plot Produce graphic Yes/No No
   
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 teh start of the
   window. The second column is the charge of the amino acids within that
   window.
   
   The output of the example above is as follows:
     _________________________________________________________________
   
CHARGE of HBB_HUMAN from 1 to 146: window 5

Position        Charge
1               0.100
2               -0.100
3               -0.400
4               -0.200
5               -0.200
6               -0.200
7               0.000
8               0.200
9               0.000
10              0.000
11              0.000
12              0.000
13              0.200
14              0.200
15              0.200
16              0.200
17              0.000
18              -0.400
19              -0.400
20              -0.400
21              -0.400
22              -0.400
23              -0.200
24              -0.200
25              -0.200
26              0.000
27              0.200
28              0.200
29              0.200
30              0.200
31              0.000
32              0.000
33              0.000
34              0.000
35              0.000
36              0.200
37              0.200
38              0.200
39              0.000
40              0.000
41              -0.200
42              -0.200
43              -0.400
44              -0.200
45              -0.200
46              -0.200
47              -0.200
48              -0.200
49              -0.200
50              -0.200
51              -0.200
52              -0.200
53              0.000
54              0.000
55              0.200
56              0.200
57              0.400
58              0.400
59              0.500
60              0.300
61              0.500
62              0.500
63              0.500
64              0.400
65              0.400
66              0.200
67              0.000
68              0.000
69              -0.200
70              -0.200
71              -0.200
72              -0.200
73              -0.100
74              0.100
75              -0.100
76              -0.100
77              -0.100
78              0.000
79              0.000
80              0.200
81              0.200
82              0.200
83              0.000
84              0.000
85              0.000
86              -0.200
87              -0.200
88              -0.100
89              -0.100
90              -0.300
91              0.100
92              0.100
93              0.100
94              0.100
95              0.100
96              -0.100
97              -0.300
98              -0.400
99              -0.400
100             0.000
101             0.000
102             0.200
103             0.200
104             0.200
105             0.000
106             0.000
107             0.000
108             0.000
109             0.000
110             0.000
111             0.000
112             0.100
113             0.200
114             0.200
115             0.200
116             0.400
117             0.100
118             0.000
119             0.000
120             0.000
121             -0.200
122             0.000
123             0.000
124             0.000
125             0.000
126             0.000
127             0.000
128             0.200
129             0.200
130             0.200
131             0.200
132             0.200
133             0.000
134             0.000
135             0.000
136             0.000
137             0.000
138             0.000
139             0.100
140             0.300
141             0.300
142             0.400
     _________________________________________________________________
   
Data files

   charge reads the data file 'Eamino.dat' to find the charge of the
   amino acids in the protein.
   
   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.
   
   To see the available EMBOSS data files, run:
   
% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".
   
   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata
       
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None.
   
See also

   Program name Description
   backtranseq Back translate a protein sequence
   checktrans Reports STOP codons and ORF statistics of a protein
   sequence
   compseq Counts the composition of dimer/trimer/etc words in a sequence
   emowse Protein identification by mass spectrometry
   freak Residue/base frequency table or plot
   iep Calculates the isoelectric point of a protein
   mwfilter Filter noisy molwts from mass spec output
   octanol Displays protein hydropathy
   pepinfo Plots simple amino acid properties in parallel
   pepstats Protein statistics
   pepwindow Displays protein hydropathy
   pepwindowall Displays protein hydropathy of a set of sequences
   
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
History

   Written (March 2001) - Alan Bleasby.
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
