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<HTML>
<HEAD>
  <TITLE>
  EMBOSS: charge
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
charge
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
    Function
</H2>
Protein charge plot
<H2>
    Description
</H2>

<b>charge</b> 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. 


<H2>
   Algorithm
</H2>


<b>charge</b> uses the column "charge" from the datafile
<i>Eamino.dat</i>.  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 -window (default is 5). 

<H2>
    Usage
</H2>
<b>Here is a sample session with charge</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>charge tsw:hbb_human </b>
Protein charge plot
Output file [hbb_human.charge]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>

<H2>
    Command line arguments
</H2>

<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
   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 standard output
   -filter             boolean    Read standard input, write 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

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>[-seqall]<br>(Parameter 1)</td>
<td>Protein sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>

<tr>
<td>-graph</td>
<td>Graph type</td>
<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif</td>
<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
</tr>

<tr>
<td>-outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.charge</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>-window</td>
<td>Window length</td>
<td>Integer 1 or more</td>
<td>5</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>-aadata</td>
<td>Amino acids properties and molecular weight data file</td>
<td>Data file</td>
<td>Eamino.dat</td>
</tr>

<tr>
<td>-plot</td>
<td>Produce graphic</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>

</table>

<H2>
    Input file format
</H2>

<b>charge</b> reads in a protein sequence.

<p>

<a name="input.1"></a>
<h3>Input files for usage example </h3>

'tsw:hbb_human' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:hbb_human</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
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.


<font color=red>  [Part of this file has been deleted for brevity]</font>

FT   VARIANT     141    141       A -&gt; T (in St Jacques: O(2) affinity up).
FT                                /FTId=VAR_003081.
FT   VARIANT     141    141       A -&gt; V (in Puttelange; polycythemia; O(2)
FT                                affinity up).
FT                                /FTId=VAR_003082.
FT   VARIANT     142    142       L -&gt; R (in Olmsted; unstable).
FT                                /FTId=VAR_003083.
FT   VARIANT     143    143       A -&gt; D (in Ohio; O(2) affinity up).
FT                                /FTId=VAR_003084.
FT   VARIANT     144    144       H -&gt; D (in Rancho Mirage).
FT                                /FTId=VAR_003085.
FT   VARIANT     144    144       H -&gt; P (in Syracuse; O(2) affinity up).
FT                                /FTId=VAR_003087.
FT   VARIANT     144    144       H -&gt; Q (in Little Rock; O(2) affinity
FT                                up).
FT                                /FTId=VAR_003086.
FT   VARIANT     144    144       H -&gt; R (in Abruzzo; O(2) affinity up).
FT                                /FTId=VAR_003088.
FT   VARIANT     145    145       K -&gt; E (in Mito; O(2) affinity up).
FT                                /FTId=VAR_003089.
FT   VARIANT     146    146       Y -&gt; C (in Rainier; O(2) affinity up).
FT                                /FTId=VAR_003090.
FT   VARIANT     146    146       Y -&gt; H (in Bethesda; O(2) affinity up).
FT                                /FTId=VAR_003091.
FT   VARIANT     147    147       H -&gt; D (in Hiroshima; O(2) affinity up).
FT                                /FTId=VAR_003092.
FT   VARIANT     147    147       H -&gt; L (in Cowtown; O(2) affinity up).
FT                                /FTId=VAR_003093.
FT   VARIANT     147    147       H -&gt; P (in York; O(2) affinity up).
FT                                /FTId=VAR_003094.
FT   VARIANT     147    147       H -&gt; 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
//
</pre>
</td></tr></table><p>


<H2>
    Output file format
</H2>

If the option '-plot' is specified then <b>charge</b> 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. 

<p>

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. 

<p>

<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: hbb_human.charge</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
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


<font color=red>  [Part of this file has been deleted for brevity]</font>

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
</pre>
</td></tr></table><p>

<H2>
    Data files
</H2>

<b>charge</b> reads the data file 'Eamino.dat' to find the charge of
the amino acids in the protein.

<p>
<p>
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.

<p>

To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:

<pre>

% embossdata -fetch -file Exxx.dat

</pre>
<p>

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".

<p>
The directories are searched in the following order:

<ul>
   <li> . (your current directory)
   <li> .embossdata (under your current directory)
   <li> ~/ (your home directory)
   <li> ~/.embossdata
</ul>
<p>


<H2>
    Notes
</H2>

None.

<H2>
    References
</H2>

None.

<H2>
    Warnings
</H2>

None.

<H2>
    Diagnostic Error Messages
</H2>

None.

<H2>
    Exit status
</H2>

It always exits with status 0.

<H2>
    Known bugs
</H2>

None.

<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="backtranambig.html">backtranambig</a></td>
<td>Back translate a protein sequence to ambiguous codons</td>
</tr>

<tr>
<td><a href="backtranseq.html">backtranseq</a></td>
<td>Back translate a protein sequence</td>
</tr>

<tr>
<td><a href="checktrans.html">checktrans</a></td>
<td>Reports STOP codons and ORF statistics of a protein</td>
</tr>

<tr>
<td><a href="compseq.html">compseq</a></td>
<td>Count composition of dimer/trimer/etc words in a sequence</td>
</tr>

<tr>
<td><a href="emowse.html">emowse</a></td>
<td>Protein identification by mass spectrometry</td>
</tr>

<tr>
<td><a href="freak.html">freak</a></td>
<td>Residue/base frequency table or plot</td>
</tr>

<tr>
<td><a href="iep.html">iep</a></td>
<td>Calculates the isoelectric point of a protein</td>
</tr>

<tr>
<td><a href="mwcontam.html">mwcontam</a></td>
<td>Shows molwts that match across a set of files</td>
</tr>

<tr>
<td><a href="mwfilter.html">mwfilter</a></td>
<td>Filter noisy molwts from mass spec output</td>
</tr>

<tr>
<td><a href="octanol.html">octanol</a></td>
<td>Displays protein hydropathy</td>
</tr>

<tr>
<td><a href="pepinfo.html">pepinfo</a></td>
<td>Plots simple amino acid properties in parallel</td>
</tr>

<tr>
<td><a href="pepstats.html">pepstats</a></td>
<td>Protein statistics</td>
</tr>

<tr>
<td><a href="pepwindow.html">pepwindow</a></td>
<td>Displays protein hydropathy</td>
</tr>

<tr>
<td><a href="pepwindowall.html">pepwindowall</a></td>
<td>Displays protein hydropathy of a set of sequences</td>
</tr>

</table>



<H2>
    Author(s)
</H2>
Alan Bleasby (ajb&nbsp;&copy;&nbsp;ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK



<H2>
    History
</H2>


Written (March 2001) - Alan Bleasby.

<H2>
    Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
None

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