charge



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Function

   Draw a protein charge plot

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

   Here is a sample session with charge


% charge tsw:hbb_human
Draw a protein charge plot
Output file [hbb_human.charge]:


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Draw a protein charge plot
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-seqall]            seqall     Protein sequence(s) filename and optional
                                  format, or reference (input USA)
*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)
*  -outfile            outfile    [*.charge] Output file name

   Additional (Optional) qualifiers:
   -window             integer    [5] Window length (Integer 1 or more)

   Advanced (Unprompted) qualifiers:
   -aadata             datafile   [Eamino.dat] Amino acids properties and
                                  molecular weight data file
   -plot               toggle     [N] Produce graphic

   Associated qualifiers:

   "-seqall" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


Input file format

   charge reads in a protein sequence.

  Input files for usage example

   'tsw:hbb_human' is a sequence entry in the example protein database
   'tsw'

  Database entry: tsw:hbb_human

ID   HBB_HUMAN               Reviewed;         147 AA.
AC   P68871; A4GX73; B2ZUE0; P02023; Q13852; Q14481; Q14510; Q45KT0;
AC   Q549N7; Q6FI08; Q6R7N2; Q8IZI1; Q9BX96; Q9UCD6; Q9UCP8; Q9UCP9;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 2.
DT   13-JUN-2012, entry version 108.
DE   RecName: Full=Hemoglobin subunit beta;
DE   AltName: Full=Beta-globin;
DE   AltName: Full=Hemoglobin beta chain;
DE   Contains:
DE     RecName: Full=LVV-hemorphin-7;
GN   Name=HBB;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=77126403; PubMed=1019344;
RA   Marotta C., Forget B., Cohen-Solal M., Weissman S.M.;
RT   "Nucleotide sequence analysis of coding and noncoding regions of human
RT   beta-globin mRNA.";
RL   Prog. Nucleic Acid Res. Mol. Biol. 19:165-175(1976).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=81064667; PubMed=6254664; DOI=10.1016/0092-8674(80)90428-6;
RA   Lawn R.M., Efstratiadis A., O'Connell C., Maniatis T.;
RT   "The nucleotide sequence of the human beta-globin gene.";
RL   Cell 21:647-651(1980).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT LYS-7.
RX   PubMed=16175509; DOI=10.1086/491748;
RA   Wood E.T., Stover D.A., Slatkin M., Nachman M.W., Hammer M.F.;
RT   "The beta-globin recombinational hotspot reduces the effects of strong
RT   selection around HbC, a recently arisen mutation providing resistance
RT   to malaria.";
RL   Am. J. Hum. Genet. 77:637-642(2005).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Lu L., Hu Z.H., Du C.S., Fu Y.S.;
RT   "DNA sequence of the human beta-globin gene isolated from a healthy
RT   Chinese.";
RL   Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT ARG-113.
RA   Cabeda J.M., Correia C., Estevinho A., Cardoso C., Amorim M.L.,
RA   Cleto E., Vale L., Coimbra E., Pinho L., Justica B.;
RT   "Unexpected patterns of globin mutations in thalassemia patients from
RT   north of Portugal.";


  [Part of this file has been deleted for brevity]

FT   VARIANT     141    141       A -> V (in Puttelange; polycythemia; O(2)
FT                                affinity up).
FT                                /FTId=VAR_003082.
FT   VARIANT     142    142       L -> R (in Olmsted; unstable).
FT                                /FTId=VAR_003083.
FT   VARIANT     143    143       A -> D (in Ohio; O(2) affinity up).
FT                                /FTId=VAR_003084.
FT   VARIANT     144    144       H -> D (in Rancho Mirage).
FT                                /FTId=VAR_003085.
FT   VARIANT     144    144       H -> P (in Syracuse; O(2) affinity up).
FT                                /FTId=VAR_003087.
FT   VARIANT     144    144       H -> Q (in Little Rock; O(2) affinity
FT                                up).
FT                                /FTId=VAR_003086.
FT   VARIANT     144    144       H -> R (in Abruzzo; O(2) affinity up).
FT                                /FTId=VAR_003088.
FT   VARIANT     145    145       K -> E (in Mito; O(2) affinity up).
FT                                /FTId=VAR_003089.
FT   VARIANT     146    146       Y -> C (in Rainier; O(2) affinity up).
FT                                /FTId=VAR_003090.
FT   VARIANT     146    146       Y -> H (in Bethesda; O(2) affinity up).
FT                                /FTId=VAR_003091.
FT   VARIANT     147    147       H -> D (in Hiroshima; O(2) affinity up).
FT                                /FTId=VAR_003092.
FT   VARIANT     147    147       H -> L (in Cowtown; O(2) affinity up).
FT                                /FTId=VAR_003093.
FT   VARIANT     147    147       H -> P (in York; O(2) affinity up).
FT                                /FTId=VAR_003094.
FT   VARIANT     147    147       H -> Q (in Kodaira; O(2) affinity up).
FT                                /FTId=VAR_003095.
FT   CONFLICT     26     26       Missing (in Ref. 15; ACD39349).
FT   CONFLICT     42     42       F -> L (in Ref. 13; AAR96398).
FT   HELIX         6     16
FT   TURN         21     23
FT   HELIX        24     35
FT   HELIX        37     42
FT   HELIX        44     46
FT   HELIX        52     57
FT   HELIX        59     77
FT   TURN         78     80
FT   HELIX        82     94
FT   TURN         95     97
FT   HELIX       102    119
FT   HELIX       120    122
FT   HELIX       125    142
FT   HELIX       144    146
SQ   SEQUENCE   147 AA;  15998 MW;  A31F6D621C6556A1 CRC64;
     MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
     VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG
     KEFTPPVQAA YQKVVAGVAN ALAHKYH
//

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.

  Output files for usage example

  File: hbb_human.charge

CHARGE of HBB_HUMAN from 1 to 147: window 5

Position        Residue Charge
1               M       0.100
2               V       0.100
3               H       -0.100
4               L       -0.400
5               T       -0.200
6               P       -0.200
7               E       -0.200
8               E       0.000
9               K       0.200
10              S       0.000
11              A       0.000
12              V       0.000
13              T       0.000
14              A       0.200
15              L       0.200
16              W       0.200
17              G       0.200
18              K       0.000
19              V       -0.400
20              N       -0.400
21              V       -0.400
22              D       -0.400
23              E       -0.400
24              V       -0.200
25              G       -0.200
26              G       -0.200
27              E       0.000
28              A       0.200
29              L       0.200
30              G       0.200
31              R       0.200
32              L       0.000
33              L       0.000
34              V       0.000
35              V       0.000
36              Y       0.000
37              P       0.200
38              W       0.200
39              T       0.200
40              Q       0.000
41              R       0.000
42              F       -0.200
43              F       -0.200
44              E       -0.400
45              S       -0.200
46              F       -0.200
47              G       -0.200


  [Part of this file has been deleted for brevity]

93              H       0.100
94              C       0.100
95              D       0.100
96              K       0.100
97              L       -0.100
98              H       -0.300
99              V       -0.400
100             D       -0.400
101             P       0.000
102             E       0.000
103             N       0.200
104             F       0.200
105             R       0.200
106             L       0.000
107             L       0.000
108             G       0.000
109             N       0.000
110             V       0.000
111             L       0.000
112             V       0.000
113             C       0.100
114             V       0.200
115             L       0.200
116             A       0.200
117             H       0.400
118             H       0.100
119             F       0.000
120             G       0.000
121             K       0.000
122             E       -0.200
123             F       0.000
124             T       0.000
125             P       0.000
126             P       0.000
127             V       0.000
128             Q       0.000
129             A       0.200
130             A       0.200
131             Y       0.200
132             Q       0.200
133             K       0.200
134             V       0.000
135             V       0.000
136             A       0.000
137             G       0.000
138             V       0.000
139             A       0.000
140             N       0.100
141             A       0.300
142             L       0.300
143             A       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
   hmoment          Calculate and plot hydrophobic moment for protein sequence(s)
   iep              Calculate the isoelectric point of proteins
   octanol          Draw a White-Wimley protein hydropathy plot
   pepinfo          Plot amino acid properties of a protein sequence in parallel
   pepstats         Calculate statistics of protein properties
   pepwindow        Draw a hydropathy plot for a protein sequence
   pepwindowall     Draw Kyte-Doolittle hydropathy plot for a protein
                    alignment

Author(s)

   Alan Bleasby
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

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

   None