|   | charge | 
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.
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.
| % 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
| 
   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,
                                  tekt, tek, none, data, xterm, png, gif)
*  -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
   -sformat1           string     Input sequence format
   -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. 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
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-seqall] (Parameter 1) | Protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | 
| -graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11 | 
| -outfile | Output file name | Output file | <*>.charge | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| -window | Window length | Integer 1 or more | 5 | 
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -aadata | Amino acids properties and molecular weight data file | Data file | Eamino.dat | 
| -plot | Produce graphic | Toggle value Yes/No | No | 
| 
ID   HBB_HUMAN               Reviewed;         147 AA.
AC   P68871; P02023; Q13852; Q14481; Q14510; Q45KT0; Q6FI08; Q8IZI1;
AC   Q9BX96; Q9UCP8; Q9UCP9;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 2.
DT   20-MAR-2007, entry version 43.
DE   Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin).
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.
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   [2]
RP   NUCLEOTIDE SEQUENCE.
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   [3]
RP   NUCLEOTIDE SEQUENCE.
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   [4]
RP   NUCLEOTIDE SEQUENCE, AND VARIANT DURHAM-N.C. PRO-115.
RC   TISSUE=Blood;
RA   Kutlar F., Abboud M., Leithner C., Holley L., Brisco J., Kutlar A.;
RT   "Electrophoretically silent, very unstable, thalassemic mutation at
RT   codon 114 of beta globin (hemoglobin Durham-N.C.) detected by cDNA
RT   sequencing of mRNA, from a Russian women.";
RL   Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   NUCLEOTIDE SEQUENCE, AND VARIANT LOUISVILLE LEU-43.
RC   TISSUE=Blood;
RA   Kutlar F., Harbin J., Brisco J., Kutlar A.;
RT   "Rapid detection of electrophoretically silent, unstable human
RT   hemoglobin 'Louisville', (Beta; Phe 42 Leu/TTT to CTT) by cDNA
RT   sequencing of mRNA.";
RL   Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases.
RN   [6]
RP   NUCLEOTIDE SEQUENCE, AND VARIANT TY GARD GLN-125.
  [Part of this file has been deleted for brevity]
FT   VARIANT     141    141       A -> T (in St Jacques: O(2) affinity up).
FT                                /FTId=VAR_003081.
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   HELIX         5     15
FT   TURN         20     22
FT   HELIX        23     34
FT   HELIX        36     41
FT   HELIX        43     45
FT   HELIX        51     56
FT   HELIX        58     76
FT   TURN         77     79
FT   HELIX        81     93
FT   TURN         94     96
FT   HELIX       101    118
FT   HELIX       119    121
FT   HELIX       124    141
FT   HELIX       143    145
SQ   SEQUENCE   147 AA;  15998 MW;  A31F6D621C6556A1 CRC64;
     MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
     VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG
     KEFTPPVQAA YQKVVAGVAN ALAHKYH
//
 | 
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.
| 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 | 
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:
| Program name | Description | 
|---|---|
| backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence | 
| backtranseq | Back-translate a protein sequence to a nucleotide sequence | 
| checktrans | Reports STOP codons and ORF statistics of a protein | 
| compseq | Calculate the composition of unique words in sequences | 
| emowse | Search protein sequences by digest fragment molecular weight | 
| freak | Generate residue/base frequency table or plot | 
| iep | Calculate the isoelectric point of proteins | 
| mwcontam | Find weights common to multiple molecular weights files | 
| mwfilter | Filter noisy data from molecular weights file | 
| octanol | Draw a White-Wimley protein hydropathy plot | 
| pepinfo | Plot amino acid properties of a protein sequence in parallel | 
| pepstats | Calculates statistics of protein properties | 
| pepwindow | Draw a Kyte-Doolittle hydropathy plot for a protein sequence | 
| pepwindowall | Draw Kyte-Doolittle hydropathy plot for a protein alignment | 
| wordcount | Count and extract unique words in DNA sequence(s) |