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charge |
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Function
Draw a protein charge plotDescription
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
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-seqall] (Parameter 1) |
seqall | Protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| -graph | xygraph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg | EMBOSS_GRAPHICS value, or x11 |
| -outfile | outfile | Output file name | Output file | <*>.charge |
| Additional (Optional) qualifiers | ||||
| -window | integer | Window length | Integer 1 or more | 5 |
| Advanced (Unprompted) qualifiers | ||||
| -aadata | datafile | Amino acids properties and molecular weight data file | Data file | Eamino.dat |
| -plot | toggle | Produce graphic | Toggle value Yes/No | No |
| Associated qualifiers | ||||
| "-seqall" associated seqall qualifiers | ||||
| -sbegin1 -sbegin_seqall |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send1 -send_seqall |
integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_seqall |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_seqall |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_seqall |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_seqall |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_seqall |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_seqall |
boolean | Make upper case | Boolean value Yes/No | N |
| -scircular1 -scircular_seqall |
boolean | Sequence is circular | Boolean value Yes/No | N |
| -squick1 -squick_seqall |
boolean | Read id and sequence only | Boolean value Yes/No | N |
| -sformat1 -sformat_seqall |
string | Input sequence format | Any string | |
| -iquery1 -iquery_seqall |
string | Input query fields or ID list | Any string | |
| -ioffset1 -ioffset_seqall |
integer | Input start position offset | Any integer value | 0 |
| -sdbname1 -sdbname_seqall |
string | Database name | Any string | |
| -sid1 -sid_seqall |
string | Entryname | Any string | |
| -ufo1 -ufo_seqall |
string | UFO features | Any string | |
| -fformat1 -fformat_seqall |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_seqall |
string | Features file name | Any string | |
| "-graph" associated xygraph qualifiers | ||||
| -gprompt | boolean | Graph prompting | Boolean value Yes/No | N |
| -gdesc | string | Graph description | Any string | |
| -gtitle | string | Graph title | Any string | |
| -gsubtitle | string | Graph subtitle | Any string | |
| -gxtitle | string | Graph x axis title | Any string | |
| -gytitle | string | Graph y axis title | Any string | |
| -goutfile | string | Output file for non interactive displays | Any string | |
| -gdirectory | string | Output directory | Any string | |
| "-outfile" associated outfile qualifiers | ||||
| -odirectory | string | Output directory | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
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
//
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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 BleasbyEuropean Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.