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<HTML>

<HEAD>
  <TITLE>
  EMBOSS: dottup
  </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">
dottup
</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>
Display a wordmatch dotplot of two sequences
<H2>
    Description
</H2>

A dotplot is a graphical representation of the regions of similarity
between two sequences.

<p> 

The two sequences are placed on the axes of a rectangular image and
(in the simplest forms of dotplot) wherever there is a similarity
between the sequences a dot is placed on the image. 

<p> 

Where the two sequences have substantial regions of similarity, many
dots align to form diagonal lines.  It is therefore possible to see at a
glance where there are local regions of similarity as these will have
long diagonal lines.  It is also easy to see other features such as
repeats (which form parallel diagonal lines), and insertions or
deletions (which form breaks or discontinuities in the diagonal lines). 

<p>

<b>dottup</b> looks for places where words (tuples) of a specified
length have an exact match in both sequences and draws a diagonal line
over the position of these words.  This is a fast, but not especially
sensitive way of creating dotplots.  It is an acceptable method for
displaying regions of substantial similarity between two sequences. 

<p>

Using a longer word (tuple) size displays less random noise, runs
extremely quickly, but is less sensitive.  Shorter word sizes are more
sensitive to shorter or fragmentary regions of similarity, but also
display more random points of similarity (noise) and runs slower. 

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

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

% <b>dottup tembl:j01636 tembl:v00294 -wordsize=6 -gtitle="v00294 vs j01636" -graph cps </b>
Display a wordmatch dotplot of two sequences

Created dottup.ps

</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>
Display a wordmatch dotplot of two sequences
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-asequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
  [-bsequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
   -wordsize           integer    [10] Word size (Integer 2 or more)
*  -graph              graph      [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)
*  -xygraph            xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)

   Additional (Optional) qualifiers (* if not always prompted):
*  -[no]boxit          boolean    [Y] Draw a box around dotplot

   Advanced (Unprompted) qualifiers:
   -stretch            toggle     [N] Use non-proportional axes

   Associated qualifiers:

   "-asequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the 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

   "-bsequence" associated qualifiers
   -sbegin2            integer    Start of the sequence to be used
   -send2              integer    End of the sequence to be used
   -sreverse2          boolean    Reverse (if DNA)
   -sask2              boolean    Ask for begin/end/reverse
   -snucleotide2       boolean    Sequence is nucleotide
   -sprotein2          boolean    Sequence is protein
   -slower2            boolean    Make lower case
   -supper2            boolean    Make upper case
   -scircular2         boolean    Sequence is circular
   -squick2            boolean    Read id and sequence only
   -sformat2           string     Input sequence format
   -iquery2            string     Input query fields or ID list
   -ioffset2           integer    Input start position offset
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         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

   "-xygraph" 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

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

<tr bgcolor="#FFFFCC">
<td>[-bsequence]<br>(Parameter 2)</td>
<td>sequence</td>
<td>Sequence filename and optional format, or reference (input USA)</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-wordsize</td>
<td>integer</td>
<td>Word size</td>
<td>Integer 2 or more</td>
<td>10</td>
</tr>

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

<tr bgcolor="#FFFFCC">
<td>-[no]boxit</td>
<td>boolean</td>
<td>Draw a box around dotplot</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

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

<tr bgcolor="#FFFFCC">
<td>-stretch</td>
<td>toggle</td>
<td>Use non-proportional axes</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>

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

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

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

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

<tr bgcolor="#FFFFCC">
<td> -sreverse1<br>-sreverse_asequence</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_asequence</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_asequence</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_asequence</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_asequence</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_asequence</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_asequence</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_asequence</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_asequence</td>
<td>string</td>
<td>Input sequence format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iquery1<br>-iquery_asequence</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_asequence</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_asequence</td>
<td>string</td>
<td>Database name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

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

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

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

<tr bgcolor="#FFFFCC">
<td> -fopenfile1<br>-fopenfile_asequence</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>"-bsequence" associated sequence qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sbegin2<br>-sbegin_bsequence</td>
<td>integer</td>
<td>Start of the sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -send2<br>-send_bsequence</td>
<td>integer</td>
<td>End of the sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sreverse2<br>-sreverse_bsequence</td>
<td>boolean</td>
<td>Reverse (if DNA)</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sask2<br>-sask_bsequence</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> -snucleotide2<br>-snucleotide_bsequence</td>
<td>boolean</td>
<td>Sequence is nucleotide</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sprotein2<br>-sprotein_bsequence</td>
<td>boolean</td>
<td>Sequence is protein</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -slower2<br>-slower_bsequence</td>
<td>boolean</td>
<td>Make lower case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -supper2<br>-supper_bsequence</td>
<td>boolean</td>
<td>Make upper case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -scircular2<br>-scircular_bsequence</td>
<td>boolean</td>
<td>Sequence is circular</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -squick2<br>-squick_bsequence</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> -sformat2<br>-sformat_bsequence</td>
<td>string</td>
<td>Input sequence format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iquery2<br>-iquery_bsequence</td>
<td>string</td>
<td>Input query fields or ID list</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ioffset2<br>-ioffset_bsequence</td>
<td>integer</td>
<td>Input start position offset</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sdbname2<br>-sdbname_bsequence</td>
<td>string</td>
<td>Database name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sid2<br>-sid_bsequence</td>
<td>string</td>
<td>Entryname</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ufo2<br>-ufo_bsequence</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fformat2<br>-fformat_bsequence</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fopenfile2<br>-fopenfile_bsequence</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 graph 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>Dottup: $(asequence.usa) vs $(bsequence.usa)</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>$(asequence.name)</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gytitle</td>
<td>string</td>
<td>Graph y axis title</td>
<td>Any string</td>
<td>$(bsequence.name)</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>"-xygraph" 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>Dottup (stretched): $(asequence.usa) vs $(bsequence.usa)</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>$(asequence.name)</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gytitle</td>
<td>string</td>
<td>Graph y axis title</td>
<td>Any string</td>
<td>$(bsequence.name)</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">
<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>dottup</b> reads two nucleotide or 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>

'tembl:j01636' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:j01636</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   J01636; SV 1; linear; genomic DNA; STD; PRO; 7477 BP.
XX
AC   J01636; J01637; K01483; K01793;
XX
DT   30-NOV-1990 (Rel. 26, Created)
DT   09-SEP-2004 (Rel. 81, Last updated, Version 8)
XX
DE   E.coli lactose operon with lacI, lacZ, lacY and lacA genes.
XX
KW   acetyltransferase; beta-D-galactosidase; galactosidase; lac operon;
KW   lac repressor protein; lacA gene; lacI gene; lactose permease; lacY gene;
KW   lacZ gene; mutagenesis; palindrome; promoter region;
KW   thiogalactoside acetyltransferase.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC   Enterobacteriaceae; Escherichia.
XX
RN   [1]
RP   1243-1266
RX   DOI; 10.1073/pnas.70.12.3581.
RX   PUBMED; 4587255.
RA   Gilbert W., Maxam A.;
RT   "The nucleotide sequence of the lac operator";
RL   Proc. Natl. Acad. Sci. U.S.A. 70(12):3581-3584(1973).
XX
RN   [2]
RP   1246-1308
RX   DOI; 10.1073/pnas.70.12.3585.
RX   PUBMED; 4587256.
RA   Maizels N.M.;
RT   "The nucleotide sequence of the lactose messenger ribonucleic acid
RT   transcribed from the UV5 promoter mutant of Escherichia coli";
RL   Proc. Natl. Acad. Sci. U.S.A. 70(12):3585-3589(1973).
XX
RN   [3]
RX   PUBMED; 4598642.
RA   Gilbert W., Maizels N., Maxam A.;
RT   "Sequences of controlling regions of the lactose operon";
RL   Cold Spring Harb. Symp. Quant. Biol. 38:845-855(1974).
XX
RN   [4]
RA   Gilbert W., Gralla J., Majors A.J., Maxam A.;
RT   "Lactose operator sequences and the action of lac repressor";
RL   (in) Sund H., Blauer G. (Eds.);
RL   PROTEIN-LIGAND INTERACTIONS:193-207;
RL   Walter de Gruyter, New York (1975)
XX
RN   [5]
RP   1146-1282


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

     cgatttggct acatgacatc aaccatatca gcaaaagtga tacgggtatt atttttgccg      4560
     ctatttctct gttctcgcta ttattccaac cgctgtttgg tctgctttct gacaaactcg      4620
     ggctgcgcaa atacctgctg tggattatta ccggcatgtt agtgatgttt gcgccgttct      4680
     ttatttttat cttcgggcca ctgttacaat acaacatttt agtaggatcg attgttggtg      4740
     gtatttatct aggcttttgt tttaacgccg gtgcgccagc agtagaggca tttattgaga      4800
     aagtcagccg tcgcagtaat ttcgaatttg gtcgcgcgcg gatgtttggc tgtgttggct      4860
     gggcgctgtg tgcctcgatt gtcggcatca tgttcaccat caataatcag tttgttttct      4920
     ggctgggctc tggctgtgca ctcatcctcg ccgttttact ctttttcgcc aaaacggatg      4980
     cgccctcttc tgccacggtt gccaatgcgg taggtgccaa ccattcggca tttagcctta      5040
     agctggcact ggaactgttc agacagccaa aactgtggtt tttgtcactg tatgttattg      5100
     gcgtttcctg cacctacgat gtttttgacc aacagtttgc taatttcttt acttcgttct      5160
     ttgctaccgg tgaacagggt acgcgggtat ttggctacgt aacgacaatg ggcgaattac      5220
     ttaacgcctc gattatgttc tttgcgccac tgatcattaa tcgcatcggt gggaaaaacg      5280
     ccctgctgct ggctggcact attatgtctg tacgtattat tggctcatcg ttcgccacct      5340
     cagcgctgga agtggttatt ctgaaaacgc tgcatatgtt tgaagtaccg ttcctgctgg      5400
     tgggctgctt taaatatatt accagccagt ttgaagtgcg tttttcagcg acgatttatc      5460
     tggtctgttt ctgcttcttt aagcaactgg cgatgatttt tatgtctgta ctggcgggca      5520
     atatgtatga aagcatcggt ttccagggcg cttatctggt gctgggtctg gtggcgctgg      5580
     gcttcacctt aatttccgtg ttcacgctta gcggccccgg cccgctttcc ctgctgcgtc      5640
     gtcaggtgaa tgaagtcgct taagcaatca atgtcggatg cggcgcgacg cttatccgac      5700
     caacatatca taacggagtg atcgcattga acatgccaat gaccgaaaga ataagagcag      5760
     gcaagctatt taccgatatg tgcgaaggct taccggaaaa aagacttcgt gggaaaacgt      5820
     taatgtatga gtttaatcac tcgcatccat cagaagttga aaaaagagaa agcctgatta      5880
     aagaaatgtt tgccacggta ggggaaaacg cctgggtaga accgcctgtc tatttctctt      5940
     acggttccaa catccatata ggccgcaatt tttatgcaaa tttcaattta accattgtcg      6000
     atgactacac ggtaacaatc ggtgataacg tactgattgc acccaacgtt actctttccg      6060
     ttacgggaca ccctgtacac catgaattga gaaaaaacgg cgagatgtac tcttttccga      6120
     taacgattgg caataacgtc tggatcggaa gtcatgtggt tattaatcca ggcgtcacca      6180
     tcggggataa ttctgttatt ggcgcgggta gtatcgtcac aaaagacatt ccaccaaacg      6240
     tcgtggcggc tggcgttcct tgtcgggtta ttcgcgaaat aaacgaccgg gataagcact      6300
     attatttcaa agattataaa gttgaatcgt cagtttaaat tataaaaatt gcctgatacg      6360
     ctgcgcttat caggcctaca agttcagcga tctacattag ccgcatccgg catgaacaaa      6420
     gcgcaggaac aagcgtcgca tcatgcctct ttgacccaca gctgcggaaa acgtactggt      6480
     gcaaaacgca gggttatgat catcagccca acgacgcaca gcgcatgaaa tgcccagtcc      6540
     atcaggtaat tgccgctgat actacgcagc acgccagaaa accacggggc aagcccggcg      6600
     atgataaaac cgattccctg cataaacgcc accagcttgc cagcaatagc cggttgcaca      6660
     gagtgatcga gcgccagcag caaacagagc ggaaacgcgc cgcccagacc taacccacac      6720
     accatcgccc acaataccgg caattgcatc ggcagccaga taaagccgca gaaccccacc      6780
     agttgtaaca ccagcgccag cattaacagt ttgcgccgat cctgatggcg agccatagca      6840
     ggcatcagca aagctcctgc ggcttgccca agcgtcatca atgccagtaa ggaaccgctg      6900
     tactgcgcgc tggcaccaat ctcaatatag aaagcgggta accaggcaat caggctggcg      6960
     taaccgccgt taatcagacc gaagtaaaca cccagcgtcc acgcgcgggg agtgaatacc      7020
     acgcgaaccg gagtggttgt tgtcttgtgg gaagaggcga cctcgcgggc gctttgccac      7080
     caccaggcaa agagcgcaac aacggcaggc agcgccacca ggcgagtgtt tgataccagg      7140
     tttcgctatg ttgaactaac cagggcgtta tggcggcacc aagcccaccg ccgcccatca      7200
     gagccgcgga ccacagcccc atcaccagtg gcgtgcgctg ctgaaaccgc cgtttaatca      7260
     ccgaagcatc accgcctgaa tgatgccgat ccccacccca ccaagcagtg cgctgctaag      7320
     cagcagcgca ctttgcgggt aaagctcacg catcaatgca ccgacggcaa tcagcaacag      7380
     actgatggcg acactgcgac gttcgctgac atgctgatga agccagcttc cggccagcgc      7440
     cagcccgccc atggtaacca ccggcagagc ggtcgac                               7477
//
</pre>
</td></tr></table><p>
<p><h3>Database entry: tembl:v00294</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   V00294; SV 1; linear; genomic DNA; STD; PRO; 1113 BP.
XX
AC   V00294;
XX
DT   09-JUN-1982 (Rel. 01, Created)
DT   10-FEB-1999 (Rel. 58, Last updated, Version 2)
XX
DE   E. coli laci gene (codes for the lac repressor).
XX
KW   DNA binding protein; repressor.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC   Enterobacteriaceae; Escherichia.
XX
RN   [1]
RP   1-1113
RX   DOI; 10.1038/274765a0.
RX   PUBMED; 355891.
RA   Farabaugh P.J.;
RT   "Sequence of the lacI gene";
RL   Nature 274(5673):765-769(1978).
XX
CC   KST ECO.LACI
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1113
FT                   /organism="Escherichia coli"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:562"
FT   CDS             31..1113
FT                   /transl_table=11
FT                   /note="reading frame"
FT                   /db_xref="GOA:P03023"
FT                   /db_xref="InterPro:IPR000843"
FT                   /db_xref="InterPro:IPR010982"
FT                   /db_xref="PDB:1CJG"
FT                   /db_xref="PDB:1EFA"
FT                   /db_xref="PDB:1JWL"
FT                   /db_xref="PDB:1JYE"
FT                   /db_xref="PDB:1JYF"
FT                   /db_xref="PDB:1L1M"
FT                   /db_xref="PDB:1LBG"
FT                   /db_xref="PDB:1LBH"
FT                   /db_xref="PDB:1LBI"
FT                   /db_xref="PDB:1LCC"
FT                   /db_xref="PDB:1LCD"
FT                   /db_xref="PDB:1LQC"
FT                   /db_xref="PDB:1LTP"
FT                   /db_xref="PDB:1OSL"
FT                   /db_xref="PDB:1TLF"
FT                   /db_xref="PDB:1Z04"
FT                   /db_xref="PDB:2BJC"
FT                   /db_xref="PDB:2KEI"
FT                   /db_xref="PDB:2KEJ"
FT                   /db_xref="PDB:2KEK"
FT                   /db_xref="PDB:2P9H"
FT                   /db_xref="PDB:2PAF"
FT                   /db_xref="PDB:2PE5"
FT                   /db_xref="PDB:3EDC"
FT                   /db_xref="UniProtKB/Swiss-Prot:P03023"
FT                   /protein_id="CAA23569.1"
FT                   /translation="MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAEL
FT                   NYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGV
FT                   EACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSH
FT                   EDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSA
FT                   MSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSC
FT                   YIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPR
FT                   ALADSLMQLARQVSRLESGQ"
XX
SQ   Sequence 1113 BP; 249 A; 304 C; 322 G; 238 T; 0 other;
     ccggaagaga gtcaattcag ggtggtgaat gtgaaaccag taacgttata cgatgtcgca        60
     gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg tgaaccaggc cagccacgtt       120
     tctgcgaaaa cgcgggaaaa agtggaagcg gcgatggcgg agctgaatta cattcccaac       180
     cgcgtggcac aacaactggc gggcaaacag tcgttgctga ttggcgttgc cacctccagt       240
     ctggccctgc acgcgccgtc gcaaattgtc gcggcgatta aatctcgcgc cgatcaactg       300
     ggtgccagcg tggtggtgtc gatggtagaa cgaagcggcg tcgaagcctg taaagcggcg       360
     gtgcacaatc ttctcgcgca acgcgtcagt gggctgatca ttaactatcc gctggatgac       420
     caggatgcca ttgctgtgga agctgcctgc actaatgttc cggcgttatt tcttgatgtc       480
     tctgaccaga cacccatcaa cagtattatt ttctcccatg aagacggtac gcgactgggc       540
     gtggagcatc tggtcgcatt gggtcaccag caaatcgcgc tgttagcggg cccattaagt       600
     tctgtctcgg cgcgtctgcg tctggctggc tggcataaat atctcactcg caatcaaatt       660
     cagccgatag cggaacggga aggcgactgg agtgccatgt ccggttttca acaaaccatg       720
     caaatgctga atgagggcat cgttcccact gcgatgctgg ttgccaacga tcagatggcg       780
     ctgggcgcaa tgcgcgccat taccgagtcc gggctgcgcg ttggtgcgga tatctcggta       840
     gtgggatacg acgataccga agacagctca tgttatatcc cgccgtcaac caccatcaaa       900
     caggattttc gcctgctggg gcaaaccagc gtggaccgct tgctgcaact ctctcagggc       960
     caggcggtga agggcaatca gctgttgccc gtctcactgg tgaaaagaaa aaccaccctg      1020
     gcgcccaata cgcaaaccgc ctctccccgc gcgttggccg attcattaat gcagctggca      1080
     cgacaggttt cccgactgga aagcgggcag tga                                   1113
//
</pre>
</td></tr></table><p>

<H2>
    Output file format
</H2>

<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>Graphics File: dottup.ps</h3>
<p><img src="dottup.1.dottup.gif" alt="[dottup results]">

<H2>
    Data files
</H2>

None.


<H2>
    Notes
</H2>

None.


<H2>
    References
</H2>

None.


<H2>
    Warnings
</H2>

None.


<H2>
    Diagnostic Error Messages
</H2>

None.


<H2>
    Exit status
</H2>


0 upon successful completion.

<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="dotmatcher.html">dotmatcher</a></td>
<td>Draw a threshold dotplot of two sequences</td>
</tr>

<tr>
<td><a href="dotpath.html">dotpath</a></td>
<td>Draw a non-overlapping wordmatch dotplot of two sequences</td>
</tr>

<tr>
<td><a href="polydot.html">polydot</a></td>
<td>Draw dotplots for all-against-all comparison of a sequence set</td>
</tr>

</table>

<p>

<a href="dotmatcher.html">dotmatcher,</a> by comparison, moves a
window of specified length up each diagonal and displays a line over
the window if the sum of the comparisons (using a substitution matrix)
exceeds a threshold. It is slower but much more sensitive.

<H2>
    Author(s)
</H2>
Ian Longden formerly at:
<br>
Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, 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 24th March 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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