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<HTML>
<HEAD>
<TITLE>
EMBOSS: polydot
</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">
polydot
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Displays all-against-all dotplots of a set of 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
(subject to threshold conditions) 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.
<p>
polydot compares all sequences in a set of sequences, draws a dotplot
for each pair of sequences by marking where words (tuples) of a
specified length have an exact match in both sequences and optionally
reports all identical matches to feature files.
<H2>
Usage
</H2>
<b>Here is a sample session with polydot</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>polydot globins.fasta -gtitle="Polydot of globins.fasta" -graph cps </b>
Displays all-against-all dotplots of a set of sequences
Word size [6]: <b></b>
Created polydot.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>
Standard (Mandatory) qualifiers (* if not always prompted):
[-sequences] seqset File containing a sequence alignment
-wordsize integer [6] Word size (Integer 2 or more)
* -outfeat featout [unknown.gff] Output features UFO
-graph graph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tekt, tek, none, data, xterm, png, gif)
Additional (Optional) qualifiers:
-[no]boxit boolean [Y] Draw a box around each dotplot
-dumpfeat toggle [N] Dump all matches as feature files
Advanced (Unprompted) qualifiers:
-gap integer [10] This specifies the size of the gap that
is used to separate the individual dotplots
in the display. The size is measured in
residues, as displayed in the output.
(Integer 0 or more)
Associated qualifiers:
"-sequences" 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
"-outfeat" associated qualifiers
-offormat string Output feature format
-ofopenfile string Features file name
-ofextension string File name extension
-ofdirectory string Output directory
-ofname string Base file name
-ofsingle boolean Separate file for each entry
"-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
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>[-sequences]<br>(Parameter 1)</td>
<td>File containing a sequence alignment</td>
<td>Readable set of sequences</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>-wordsize</td>
<td>Word size</td>
<td>Integer 2 or more</td>
<td>6</td>
</tr>
<tr>
<td>-outfeat</td>
<td>Output features UFO</td>
<td>Writeable feature table</td>
<td><i>unknown.gff</i></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 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>-[no]boxit</td>
<td>Draw a box around each dotplot</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>
<tr>
<td>-dumpfeat</td>
<td>Dump all matches as feature files</td>
<td>Toggle value Yes/No</td>
<td>No</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>-gap</td>
<td>This specifies the size of the gap that is used to separate the individual dotplots in the display. The size is measured in residues, as displayed in the output.</td>
<td>Integer 0 or more</td>
<td>10</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>polydot</b> reads in a set of nucleic or protein sequences.
<p>
The sequences may or may not be aligned.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: globins.fasta</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
>HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
EFTPPVQAAYQKVVAGVANALAHKYH
>HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
DFTPELQASYQKVVAGVANALAHKYH
>HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
VHASLDKFLASVSTVLTSKYR
>HBA_HORSE Sw:Hba_Horse => HBA_HORSE
VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
VHASLDKFLSSVSTVLTSKYR
>MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
GDFGADAQGAMNKALELFRKDIAAKYKELGYQG
>GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
AVIADTVAAGDAGFEKLMSMICILLRSAY
>LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL
QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE
VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
A graphical image is displayed on the specified graphics device.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>Graphics File: polydot.ps</h3>
<p><img src="polydot.1.polydot.gif" alt="[polydot 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 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="dotmatcher.html">dotmatcher</a></td>
<td>Displays a thresholded dotplot of two sequences</td>
</tr>
<tr>
<td><a href="dotpath.html">dotpath</a></td>
<td>Non-overlapping wordmatch dotplot of two sequences</td>
</tr>
<tr>
<td><a href="dottup.html">dottup</a></td>
<td>Displays a wordmatch dotplot of two sequences</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Ian Longden (il © sanger.ac.uk)
<br>
Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK.
<H2>
History
</H2>
Completed 2nd June 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
</BODY>
</HTML>
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