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<HTML>

<HEAD>
  <TITLE>
  EMBOSS: iep
  </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="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
iep
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>



<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Calculate the isoelectric point of proteins

<H2>
    Description
</H2>

<p><b>iep</b> calculates the isoelectric point of a protein from its
amino acid composition assuming that no electrostatic interactions
change the propensity for ionization.  Optionally, <b>iep</b> will
plot the ionization curve with respect to pH and write an output file
of the data, where for each pH point the number of bound electrons and
charge is given.</p>

<p>For peptide fragments it is possible to exclude the charges of the
  amino and carboxy terminal residues.
</p>

<H2>
    Usage
</H2>

Here is a sample session with <b>iep</b>
<p>

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

% <b>iep tsw:laci_ecoli </b>
Calculate the isoelectric point of proteins
Output file [laci_ecoli.iep]: <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>
<p>
<b>Example 2</b>
<p>

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

% <b>iep tsw:ifna2_human -disulphide 2 -lysinemodified 2  </b>
Calculate the isoelectric point of proteins
Output file [ifna2_human.iep]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#input.2">Go to the input files for this example</a><br><a href="#output.2">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>
Calculate the isoelectric point of proteins
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          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    [*.iep] Output file name

   Additional (Optional) qualifiers:
   -amino              integer    [1] Number of N-termini (Integer 0 or more)
   -carboxyl           integer    [1] Number of C-termini (Integer 0 or more)
   -[no]termini        boolean    [Y] Include charge at N and C terminus
   -lysinemodified     integer    [0] Number of modified lysines (Integer 0 or
                                  more)
   -disulphides        integer    [0] Number of disulphide bridges (Integer 0
                                  or more)

   Advanced (Unprompted) qualifiers:
   -pkdata             datafile   [Epk.dat] Values of pKa for amino acids
   -step               float      [.5] Step value for pH (Number from 0.010 to
                                  1.000)
   -plot               toggle     [N] Plot charge vs pH
   -[no]report         toggle     [Y] Write results to a file

   Associated qualifiers:

   "-sequence" 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

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-sequence]<br>(Parameter 1)</td>
<td>seqall</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 bgcolor="#FFFFCC">
<td>-graph</td>
<td>xygraph</td>
<td>Graph type</td>
<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg</td>
<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-outfile</td>
<td>outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.iep</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-amino</td>
<td>integer</td>
<td>Number of N-termini</td>
<td>Integer 0 or more</td>
<td>1</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-carboxyl</td>
<td>integer</td>
<td>Number of C-termini</td>
<td>Integer 0 or more</td>
<td>1</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]termini</td>
<td>boolean</td>
<td>Include charge at N and C terminus</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-lysinemodified</td>
<td>integer</td>
<td>Number of modified lysines</td>
<td>Integer 0 or more</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-disulphides</td>
<td>integer</td>
<td>Number of disulphide bridges</td>
<td>Integer 0 or more</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-pkdata</td>
<td>datafile</td>
<td>Values of pKa for amino acids</td>
<td>Data file</td>
<td>Epk.dat</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-step</td>
<td>float</td>
<td>Step value for pH</td>
<td>Number from 0.010 to 1.000</td>
<td>.5</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-plot</td>
<td>toggle</td>
<td>Plot charge vs pH</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]report</td>
<td>toggle</td>
<td>Write results to a file</td>
<td>Toggle value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-sequence" associated seqall qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sbegin1<br>-sbegin_sequence</td>
<td>integer</td>
<td>Start of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -send1<br>-send_sequence</td>
<td>integer</td>
<td>End of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sreverse1<br>-sreverse_sequence</td>
<td>boolean</td>
<td>Reverse (if DNA)</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sask1<br>-sask_sequence</td>
<td>boolean</td>
<td>Ask for begin/end/reverse</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -snucleotide1<br>-snucleotide_sequence</td>
<td>boolean</td>
<td>Sequence is nucleotide</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sprotein1<br>-sprotein_sequence</td>
<td>boolean</td>
<td>Sequence is protein</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -slower1<br>-slower_sequence</td>
<td>boolean</td>
<td>Make lower case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -supper1<br>-supper_sequence</td>
<td>boolean</td>
<td>Make upper case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -scircular1<br>-scircular_sequence</td>
<td>boolean</td>
<td>Sequence is circular</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -squick1<br>-squick_sequence</td>
<td>boolean</td>
<td>Read id and sequence only</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sformat1<br>-sformat_sequence</td>
<td>string</td>
<td>Input sequence format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iquery1<br>-iquery_sequence</td>
<td>string</td>
<td>Input query fields or ID list</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ioffset1<br>-ioffset_sequence</td>
<td>integer</td>
<td>Input start position offset</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sdbname1<br>-sdbname_sequence</td>
<td>string</td>
<td>Database name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sid1<br>-sid_sequence</td>
<td>string</td>
<td>Entryname</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ufo1<br>-ufo_sequence</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fformat1<br>-fformat_sequence</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fopenfile1<br>-fopenfile_sequence</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-graph" associated xygraph qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gprompt</td>
<td>boolean</td>
<td>Graph prompting</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gdesc</td>
<td>string</td>
<td>Graph description</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gtitle</td>
<td>string</td>
<td>Graph title</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gsubtitle</td>
<td>string</td>
<td>Graph subtitle</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gxtitle</td>
<td>string</td>
<td>Graph x axis title</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gytitle</td>
<td>string</td>
<td>Graph y axis title</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -goutfile</td>
<td>string</td>
<td>Output file for non interactive displays</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gdirectory</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>




<H2>
    Input file format
</H2>

<b>iep</b> reads one or more protein sequences.
<p>
<p>

The input is a standard EMBOSS sequence query (also known as a 'USA').

<p>
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl

<p>

Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.

<p>
The input format can be specified by using the
command-line qualifier <tt>-sformat xxx</tt>, where 'xxx' is replaced
by the name of the required format.  The available format names are:
gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir
(nbrf), swissprot (swiss, sw), dasgff and debug.

<p>

See:
<A href="http://emboss.sf.net/docs/themes/SequenceFormats.html">
http://emboss.sf.net/docs/themes/SequenceFormats.html</A>
for further information on sequence formats.

<p>


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

'tsw:laci_ecoli' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:laci_ecoli</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   LACI_ECOLI              Reviewed;         360 AA.
AC   P03023; O09196; P71309; Q2MC79; Q47338;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   19-JUL-2003, sequence version 3.
DT   13-JUN-2012, entry version 136.
DE   RecName: Full=Lactose operon repressor;
GN   Name=lacI; OrderedLocusNames=b0345, JW0336;
OS   Escherichia coli (strain K12).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=78246991; PubMed=355891; DOI=10.1038/274765a0;
RA   Farabaugh P.J.;
RT   "Sequence of the lacI gene.";
RL   Nature 274:765-769(1978).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Chen J., Matthews K.K.S.M.;
RL   Submitted (MAY-1991) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Marsh S.;
RL   Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RA   Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA   Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA   Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT   "Sequence of minutes 4-25 of Escherichia coli.";
RL   Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   MEDLINE=97426617; PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
RA   Mau B., Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1474(1997).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains


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

FT   CHAIN         1    360       Lactose operon repressor.
FT                                /FTId=PRO_0000107963.
FT   DOMAIN        1     58       HTH lacI-type.
FT   DNA_BIND      6     25       H-T-H motif.
FT   VARIANT     282    282       Y -&gt; D (in T41 mutant).
FT   MUTAGEN      17     17       Y-&gt;H: Broadening of specificity.
FT   MUTAGEN      22     22       R-&gt;N: Recognizes an operator variant.
FT   CONFLICT    286    286       L -&gt; S (in Ref. 1, 4 and 7).
FT   HELIX         6     11
FT   TURN         12     14
FT   HELIX        17     24
FT   HELIX        33     45
FT   HELIX        51     56
FT   STRAND       63     69
FT   HELIX        74     89
FT   STRAND       93     98
FT   STRAND      101    103
FT   HELIX       104    115
FT   TURN        116    118
FT   STRAND      122    126
FT   HELIX       130    139
FT   TURN        140    142
FT   STRAND      145    150
FT   STRAND      154    156
FT   STRAND      158    161
FT   HELIX       163    177
FT   STRAND      181    186
FT   HELIX       192    207
FT   STRAND      213    217
FT   HELIX       222    234
FT   STRAND      240    246
FT   HELIX       247    259
FT   TURN        265    267
FT   STRAND      268    271
FT   HELIX       277    281
FT   STRAND      282    284
FT   STRAND      287    290
FT   HELIX       293    308
FT   STRAND      314    319
FT   STRAND      322    324
FT   STRAND      334    338
FT   HELIX       343    353
FT   HELIX       354    356
SQ   SEQUENCE   360 AA;  38590 MW;  347A8DEE92D736CB CRC64;
     MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RVAQQLAGKQ
     SLLIGVATSS LALHAPSQIV AAIKSRADQL GASVVVSMVE RSGVEACKAA VHNLLAQRVS
     GLIINYPLDD QDAIAVEAAC TNVPALFLDV SDQTPINSII FSHEDGTRLG VEHLVALGHQ
     QIALLAGPLS SVSARLRLAG WHKYLTRNQI QPIAEREGDW SAMSGFQQTM QMLNEGIVPT
     AMLVANDQMA LGAMRAITES GLRVGADISV VGYDDTEDSS CYIPPLTTIK QDFRLLGQTS
     VDRLLQLSQG QAVKGNQLLP VSLVKRKTTL APNTQTASPR ALADSLMQLA RQVSRLESGQ
//
</pre>
</td></tr></table><p>

<a name="input.2"></a>
<h3>Input files for usage example 2</h3>
<p><h3>Database entry: tsw:ifna2_human</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   IFNA2_HUMAN             Reviewed;         188 AA.
AC   P01563; P01564; Q14606; Q96KI6;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   21-JUL-1986, sequence version 1.
DT   16-MAY-2012, entry version 128.
DE   RecName: Full=Interferon alpha-2;
DE            Short=IFN-alpha-2;
DE   AltName: Full=Interferon alpha-A;
DE            Short=LeIF A;
DE   Flags: Precursor;
GN   Name=IFNA2;
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 / MRNA].
RX   MEDLINE=81052322; PubMed=6159538; DOI=10.1038/287411a0;
RA   Goeddel D.V., Yelverton E., Ullrich A., Heyneker H.L., Miozzari G.,
RA   Holmes W., Seeburg P.H., Dull T.J., May L., Stebbing N., Crea R.,
RA   Maeda S., McCandliss R., Sloma A., Tabor J.M., Gross M.,
RA   Familletti P.C., Pestka S.;
RT   "Human leukocyte interferon produced by E. coli is biologically
RT   active.";
RL   Nature 287:411-416(1980).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
RX   MEDLINE=81148795; PubMed=6163083; DOI=10.1038/290020a0;
RA   Goeddel D.V., Leung D.W., Dull T.J., Gross M., Lawn R.M.,
RA   McCandliss R., Seeburg P.H., Ullrich A., Yelverton E., Gray P.W.;
RT   "The structure of eight distinct cloned human leukocyte interferon
RT   cDNAs.";
RL   Nature 290:20-26(1981).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
RX   MEDLINE=82060261; PubMed=6170983; DOI=10.1073/pnas.78.9.5435;
RA   Lawn R.M., Gross M., Houck C.M., Franke A.E., Gray P.V., Goeddel D.V.;
RT   "DNA sequence of a major human leukocyte interferon gene.";
RL   Proc. Natl. Acad. Sci. U.S.A. 78:5435-5439(1981).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RC   TISSUE=Bone marrow tumor;
RX   MEDLINE=86069501; PubMed=3906813;
RA   Oliver G., Balbas P., Valle F., Soberon X., Bolivar F.;
RT   "Cloning of human leukocyte interferon cDNA and a strategy for its
RT   production in E. coli.";
RL   Rev. Latinoam. Microbiol. 27:141-150(1985).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].


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

DR   GO; GO:0060338; P:regulation of type I interferon-mediated signaling pathway; TAS:Reactome.
DR   GO; GO:0009615; P:response to virus; IEA:UniProtKB-KW.
DR   GO; GO:0060337; P:type I interferon-mediated signaling pathway; TAS:Reactome.
DR   Gene3D; G3DSA:1.20.1250.10; 4_helix_cytokine_core; 1.
DR   InterPro; IPR009079; 4_helix_cytokine-like_core.
DR   InterPro; IPR012351; 4_helix_cytokine_core.
DR   InterPro; IPR000471; Interferon_alpha/beta/delta.
DR   PANTHER; PTHR11691; Interferon_abd; 1.
DR   Pfam; PF00143; Interferon; 1.
DR   PRINTS; PR00266; INTERFERONAB.
DR   SMART; SM00076; IFabd; 1.
DR   SUPFAM; SSF47266; 4_helix_cytokine; 1.
DR   PROSITE; PS00252; INTERFERON_A_B_D; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Antiviral defense; Complete proteome; Cytokine;
KW   Direct protein sequencing; Disulfide bond; Glycoprotein;
KW   Pharmaceutical; Polymorphism; Reference proteome; Secreted; Signal.
FT   SIGNAL        1     23
FT   CHAIN        24    188       Interferon alpha-2.
FT                                /FTId=PRO_0000016360.
FT   CARBOHYD    129    129       O-linked (GalNAc...).
FT                                /FTId=CAR_000049.
FT   DISULFID     24    121
FT   DISULFID     52    161
FT   VARIANT       6      6       A -&gt; D (in dbSNP:rs35971916).
FT                                /FTId=VAR_055972.
FT   VARIANT      46     46       K -&gt; R (in alpha-2B and alpha-2C;
FT                                dbSNP:rs1061959).
FT                                /FTId=VAR_004012.
FT   VARIANT      57     57       H -&gt; R (in alpha-2C).
FT                                /FTId=VAR_013001.
FT   VARIANT     177    177       S -&gt; L (in a breast cancer sample;
FT                                somatic mutation).
FT                                /FTId=VAR_036329.
FT   HELIX        33     44
FT   TURN         49     54
FT   HELIX        63     66
FT   STRAND       67     69
FT   STRAND       71     75
FT   HELIX        76     91
FT   HELIX        93     98
FT   HELIX       101    123
FT   HELIX       134    155
FT   HELIX       160    178
FT   TURN        179    182
SQ   SEQUENCE   188 AA;  21550 MW;  101DD21D394CBF97 CRC64;
     MALTFALLVA LLVLSCKSSC SVGCDLPQTH SLGSRRTLML LAQMRKISLF SCLKDRHDFG
     FPQEEFGNQF QKAETIPVLH EMIQQIFNLF STKDSSAAWD ETLLDKFYTE LYQQLNDLEA
     CVIQGVGVTE TPLMKEDSIL AVRKYFQRIT LYLKEKKYSP CAWEVVRAEI MRSFSLSTNL
     QESLRSKE
//
</pre>
</td></tr></table><p>



<H2>
    Output file format
</H2>

With <tt>-plot</tt> specified, a graphical output is produced.

<p>

The output is to the specified graphics device.

<p>

The results can be output in one of several formats by using the
command-line qualifier <b>-graph xxx</b>, where 'xxx' is replaced by
the name of the required device. Support depends on the availability
of third-party software packages.

<p>
The device names that output to a file are:
ps (postscript), cps (colourps), png, gif, pdf, svg, hpgl, hp7470,
hp7580, das, data.

<p> The other available device names are: meta, x11 (xwindows), tek
(tek4107t), tekt (tektronix), xterm, text.

<p>
Output can be turned off by specifying none (null).

<p>

See:
<A href="http://emboss.sf.net/docs/themes/GraphicsDevices.html">
http://emboss.sf.net/docs/themes/GraphicsDevices.html</A>
for further information on supported devices.

<p>

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: laci_ecoli.iep</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
IEP of LACI_ECOLI from 1 to 360
Isoelectric Point = 6.8385

   pH     Bound    Charge
  1.00    81.96    37.96
  1.50    81.89    37.89
  2.00    81.65    37.65
  2.50    80.91    36.91
  3.00    78.79    34.79
  3.50    73.70    29.70
  4.00    65.15    21.15
  4.50    56.73    12.73
  5.00    51.75     7.75
  5.50    49.35     5.35
  6.00    47.60     3.60
  6.50    45.48     1.48
  7.00    43.37    -0.63
  7.50    41.85    -2.15
  8.00    40.66    -3.34
  8.50    39.41    -4.59
  9.00    38.01    -5.99
  9.50    36.14    -7.86
 10.00    32.99   -11.01
 10.50    28.45   -15.55
 11.00    23.58   -20.42
 11.50    19.41   -24.59
 12.00    15.19   -28.81
 12.50     9.75   -34.25
 13.00     4.64   -39.36
 13.50     1.75   -42.25
 14.00     0.59   -43.41
</pre>
</td></tr></table><p>

<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: ifna2_human.iep</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
IEP of IFNA2_HUMAN from 1 to 188
Isoelectric Point = 5.7240

   pH     Bound    Charge
  1.00    52.98    22.98
  1.50    52.93    22.93
  2.00    52.77    22.77
  2.50    52.28    22.28
  3.00    50.87    20.87
  3.50    47.47    17.47
  4.00    41.62    11.62
  4.50    35.67     5.67
  5.00    32.10     2.10
  5.50    30.46     0.46
  6.00    29.48    -0.52
  6.50    28.46    -1.54
  7.00    27.44    -2.56
  7.50    26.58    -3.42
  8.00    25.80    -4.20
  8.50    24.95    -5.05
  9.00    23.99    -6.01
  9.50    22.70    -7.30
 10.00    20.46    -9.54
 10.50    17.02   -12.98
 11.00    13.16   -16.84
 11.50    10.04   -19.96
 12.00     7.49   -22.51
 12.50     4.72   -25.28
 13.00     2.23   -27.77
 13.50     0.84   -29.16
 14.00     0.28   -29.72
</pre>
</td></tr></table><p>
<p>

For each pH point it gives the number of bound electrons and the charge.


<H2>
    Data files
</H2>

<b>iep</b> reads in local data file <em>Epk.dat</em> which contains amino acid
pK values used to calculate the isoelectric point of the whole 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>

<p>
Here is the default <em>Epk.dat</em> file:

<pre>
# pK values for amino acids
# O=Ornithine J=Hydroxyproline
#
# Amino acid	pK
Amino		8.6
Carboxyl	3.6

C		8.5
D		3.9
E		4.1
H		6.5
K		10.8
R		12.5
Y		10.1
</pre>


<H2>
    Notes
</H2>

<p>Adjusting the pH of an aqueous protein solution to the point where
the numbers of positive and negative charges on the protein are equal
brings the protein to its isoelectric point. This is often the point
of lowest solubility, presumably because it is the point at which
there are fewest intermolecular repulsions, so that the molecules tend
to form aggregates.</p>

<p>Modified lysines and disulphide bridges affect the contributions of
  those residues to the protein charge. A set number of each residue
  can be excluded.
</p>

<H2>
    References
</H2>

None.

<H2>
    Warnings
</H2>

None.

<H2>
    Diagnostic Error Messages
</H2>

None.

<H2>
    Exit status
</H2>

0 if successful.

<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="abiview.html">abiview</a></td>
<td>Display the trace in an ABI sequencer file</td>
</tr>

<tr>
<td><a href="charge.html">charge</a></td>
<td>Draw a protein charge plot</td>
</tr>

<tr>
<td><a href="cirdna.html">cirdna</a></td>
<td>Draw circular map of DNA constructs</td>
</tr>

<tr>
<td><a href="hmoment.html">hmoment</a></td>
<td>Calculate and plot hydrophobic moment for protein sequence(s)</td>
</tr>

<tr>
<td><a href="lindna.html">lindna</a></td>
<td>Draw linear maps of DNA constructs</td>
</tr>

<tr>
<td><a href="octanol.html">octanol</a></td>
<td>Draw a White-Wimley protein hydropathy plot</td>
</tr>

<tr>
<td><a href="pepinfo.html">pepinfo</a></td>
<td>Plot amino acid properties of a protein sequence in parallel</td>
</tr>

<tr>
<td><a href="pepnet.html">pepnet</a></td>
<td>Draw a helical net for a protein sequence</td>
</tr>

<tr>
<td><a href="pepstats.html">pepstats</a></td>
<td>Calculate statistics of protein properties</td>
</tr>

<tr>
<td><a href="pepwheel.html">pepwheel</a></td>
<td>Draw a helical wheel diagram for a protein sequence</td>
</tr>

<tr>
<td><a href="pepwindow.html">pepwindow</a></td>
<td>Draw a hydropathy plot for a protein sequence</td>
</tr>

<tr>
<td><a href="pepwindowall.html">pepwindowall</a></td>
<td>Draw Kyte-Doolittle hydropathy plot for a protein alignment</td>
</tr>

<tr>
<td><a href="plotorf.html">plotorf</a></td>
<td>Plot potential open reading frames in a nucleotide sequence</td>
</tr>

<tr>
<td><a href="prettyplot.html">prettyplot</a></td>
<td>Draw a sequence alignment with pretty formatting</td>
</tr>

<tr>
<td><a href="prettyseq.html">prettyseq</a></td>
<td>Write a nucleotide sequence and its translation to file</td>
</tr>

<tr>
<td><a href="remap.html">remap</a></td>
<td>Display restriction enzyme binding sites in a nucleotide sequence</td>
</tr>

<tr>
<td><a href="showfeat.html">showfeat</a></td>
<td>Display features of a sequence in pretty format</td>
</tr>

<tr>
<td><a href="showpep.html">showpep</a></td>
<td>Display protein sequences with features in pretty format</td>
</tr>

<tr>
<td><a href="sixpack.html">sixpack</a></td>
<td>Display a DNA sequence with 6-frame translation and ORFs</td>
</tr>

</table>


<H2>
    Author(s)
</H2>
Alan Bleasby 
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.

<H2>
    History
</H2>



Completed 1st August 1999.

<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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</HTML>