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README_heatlogo.html
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<div class="document" id="heatlogo">
<h1 class="title">HeatLogo</h1>
<h2 class="subtitle" id="version-1-0">version: 1.0</h2>
<div class="section" id="general-description">
<h1>General description</h1>
<p>HeatLogo is a tool for generating sequence logos from biological sequence
alignments and for coloring each symbol in the logos according to its P-value.
It can be run on the command line, as a standalone webserver, as a CGI webapp,
or as a python library.</p>
</div>
<div class="section" id="requirement">
<h1>Requirement</h1>
<p>HeatLogo requires the following environment to run:</p>
<ul class="simple">
<li>Python 2.x (x >= 5)</li>
<li>Python array package 'numpy'</li>
<li>Python scientific package 'scipy'</li>
</ul>
<p>('numpy' and 'scipy' can be freely downloaded from: <a class="reference external" href="http://www.scipy.org/Download">http://www.scipy.org/Download</a>)</p>
</div>
<div class="section" id="usage">
<h1>Usage</h1>
<p>Create sequence logos from biological sequence alignments and color symbols
according to P-values:</p>
<pre class="literal-block">
$ heatlogo [options] < sequence_data.fa > sequence_logo.eps
</pre>
</div>
<div class="section" id="options">
<h1>Options</h1>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group">
<kbd><span class="option">-h</span>, <span class="option">--help</span></kbd></td>
<td>Show all options, their default settings and exit</td></tr>
</tbody>
</table>
</blockquote>
<div class="section" id="input-output-options">
<h2>Input/Output Options</h2>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-i</span>, <span class="option">--input <var>FILENAME</var></span></kbd></td>
</tr>
<tr><td> </td><td>Sequence input file (default: stdin)</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-f</span>, <span class="option">--input-format <var>FORMAT</var></span></kbd></td>
</tr>
<tr><td> </td><td>Type of multiple sequence alignment or position weight matrix
file: (clustal, fasta, plain, msf, genbank, nbrf, nexus phylip
stockholm, intelligenetics, table, array, transfac)</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-o</span>, <span class="option">--output <var>FILENAME</var></span></kbd></td>
</tr>
<tr><td> </td><td>Output file (default: stdout)</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-F</span>, <span class="option">--output-format <var>FORMAT</var></span></kbd></td>
</tr>
<tr><td> </td><td><p class="first">Format of output: eps (default), png, png_print, pdf, jpeg, svg, logodata.</p>
<table class="last docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">--pwm-prob <var>FILENAME</var></span></kbd></td>
</tr>
<tr><td> </td><td>Output position weight matrix composed of logarithmic probabilities</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">--pwm-pval <var>FILENAME</var></span></kbd></td>
</tr>
<tr><td> </td><td>Output position weight matrix of P-values</td></tr>
</tbody>
</table>
</td></tr>
</tbody>
</table>
</blockquote>
</div>
<div class="section" id="logo-data-options">
<h2>Logo Data Options</h2>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-A</span>, <span class="option">--sequence-type <var>TYPE</var></span></kbd></td>
</tr>
<tr><td> </td><td>The type of sequence data: 'protein', 'rna', 'dna', or 'codon'
(See also: --codon-frame)</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-a</span>, <span class="option">--alphabet <var>ALPHABET</var></span></kbd></td>
</tr>
<tr><td> </td><td>The set of symbols to count, e.g. 'AGTC'. All characters not in
the alphabet are ignored. If neither the alphabet nor sequence-type
are specified then heatlogo will examine the input data and make
an educated guess. (See also: --sequence-type, --ignore-lower-case)</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-R</span>, <span class="option">--codon-frame <var>NUMBER</var></span></kbd></td>
</tr>
<tr><td> </td><td>Codon reading frame (default: +1): [+1, +2, +3] indicate the forward
strand frame, and [-1, -2, -3] indicate the reverse strand frame</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-b</span>, <span class="option">--composition <var>COMP</var></span></kbd></td>
</tr>
<tr><td> </td><td><p class="first">The expected composition of the sequences. HeatLogo accepts four
types of formats:</p>
<blockquote class="last">
<ol class="arabic simple">
<li>String: 'auto' (default), 'equiprobable', or 'none'
(do not perform any compositional adjustment, Heatmap: off).
The automatic option uses a typical distribution for
proteins and equiprobable distribution for everything else.</li>
<li>CG percentage.</li>
<li>Explicit distribution of bases, amino acids, or codons
(format: "{'A':10, 'C':40, 'G':40, 'T':10}").</li>
<li>Tab-delimited file containing each symbol and its expected
composition in each line.</li>
</ol>
</blockquote>
</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-w</span>, <span class="option">--weight <var>NUMBER</var></span></kbd></td>
</tr>
<tr><td> </td><td>The weight of prior data. Default depends on alphabet length</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-N</span>, <span class="option">--second-data <var>FILENAME</var></span></kbd></td>
</tr>
<tr><td> </td><td>Second dataset file to compare with the input. HeatLogo measures
statistical significance at each column by comparing the number of
symbols appered in input and second datasets.
Accepted formats: clustal, fasta, plain, msf, genbank, nbrf, nexus,
phylip, stockholm, intelligenetics, table, array.</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-B</span>, <span class="option">--second-composition <var>COMP</var></span></kbd></td>
</tr>
<tr><td> </td><td>The expected composition of the second sample sequences. The supported
formats are the same as those of '--composition'.</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-W</span>, <span class="option">--second-weight <var>NUMBER</var></span></kbd></td>
</tr>
<tr><td> </td><td>The prior weight for the second dataset. Default depends on alphabet length.</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-U</span>, <span class="option">--units <var>NUMBER</var></span></kbd></td>
</tr>
<tr><td> </td><td>A unit of entropy ('bits' (default), 'nats', 'digits'), or a unit of free
energy ('kT', 'kJ/mol', 'kcal/mol'), or 'probability' for probabilities</td></tr>
</tbody>
</table>
</blockquote>
</div>
<div class="section" id="heat-map-options">
<h2>Heat Map Options</h2>
<p>These options affect the format of the sequence logo in the heat map
mode (See also Color Options).</p>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-S</span>, <span class="option">--stats-test <var>TEST</var></span></kbd></td>
</tr>
<tr><td> </td><td>Specify a statistical test to calculate p-values: 'binomial', 't-test',
'z-score' (default: t-test)</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-H</span>, <span class="option">--heat-scheme <var>SCHEME</var></span></kbd></td>
</tr>
<tr><td> </td><td><dl class="first docutils">
<dt>Specify a heatmap color scheme: 'magenta-cyan', 'red-blue', 'red-green',</dt>
<dd>'thermography' (See also: '--p-color').</dd>
<dt>--p-color COLOR PVALUE Specify a color for a p-value (p-value range: -1 < p < 1).</dt>
<dd>(e.g. --p-color blue 0.5 --p-color red 0.25)</dd>
</dl>
<table class="last docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">--hide-colorkey</span></kbd></td>
</tr>
<tr><td> </td><td>Toggle switch to hide a heatmap color key on the right side of a
sequence logo (default: off)</td></tr>
</tbody>
</table>
</td></tr>
</tbody>
</table>
</blockquote>
</div>
<div class="section" id="color-options">
<h2>Color Options</h2>
<p>Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc
(See also Heat Map Options).</p>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-C</span>, <span class="option">--color-scheme <var>SCHEME</var></span></kbd></td>
</tr>
<tr><td> </td><td><dl class="first docutils">
<dt>Specify a standard color scheme (auto, base pairing, charge, chemistry,</dt>
<dd>classic, dna codon, hydrophobicity, monochrome, rna codon; Heatmap: off)</dd>
<dt>--c-color COLOR SYMBOLS DESCRIPTION</dt>
<dd><dl class="first last docutils">
<dt>Specify symbol colors (e.g. --c-color black AG 'Purine'</dt>
<dd>--c-color red TC 'Pyrimidine'; Heatmap: off)</dd>
</dl>
</dd>
</dl>
<table class="last docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">--default-color <var>COLOR</var></span></kbd></td>
</tr>
<tr><td> </td><td>Symbol color if not otherwise specified.</td></tr>
</tbody>
</table>
</td></tr>
</tbody>
</table>
</blockquote>
</div>
<div class="section" id="transformations">
<h2>Transformations</h2>
<p>Optional transformations of the sequence data.</p>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">--ignore-lower-case</span></kbd></td>
</tr>
<tr><td> </td><td>Disregard lower case letters and only count upper case letters in sequences.</td></tr>
</tbody>
</table>
<p class="attribution">—reverse Simply reverse input sequences.</p>
</blockquote>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group">
<kbd><span class="option">--complement</span></kbd></td>
<td>Complement DNA sequences.</td></tr>
</tbody>
</table>
</blockquote>
</div>
<div class="section" id="logo-format-options">
<h2>Logo Format Options</h2>
<p>These options control the format and display of the sequence logo.</p>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-I</span>, <span class="option">--first-index <var>INDEX</var></span></kbd></td>
</tr>
<tr><td> </td><td>Index of first position in sequence data (default: 1)</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-s</span>, <span class="option">--start <var>INDEX</var></span></kbd></td>
</tr>
<tr><td> </td><td>Lower bound (i.e. start position) of sequence to display</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-e</span>, <span class="option">--end <var>INDEX</var></span></kbd></td>
</tr>
<tr><td> </td><td>Upper bound (i.e. end position) of sequence to display</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-L</span>, <span class="option">--size <var>LOGOSIZE</var></span></kbd></td>
</tr>
<tr><td> </td><td>Specify a standard logo size (small, medium (default), large)</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-n</span>, <span class="option">--stacks-per-line <var>COUNT</var></span></kbd></td>
</tr>
<tr><td> </td><td>Maximum number of logo stacks per logo line (default: 40)</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-t</span>, <span class="option">--title <var>TEXT</var></span></kbd></td>
</tr>
<tr><td> </td><td>Logo title text.</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-l</span>, <span class="option">--label <var>TEXT</var></span></kbd></td>
</tr>
<tr><td> </td><td>A figure label (e.g. '2a').</td></tr>
</tbody>
</table>
<p>-X, --show-xaxis YES/NO Display sequence numbers along x-axis? (default: True)</p>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-x</span>, <span class="option">--xlabel <var>TEXT</var></span></kbd></td>
</tr>
<tr><td> </td><td><p class="first">X-axis label</p>
<table class="last docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">--annotate <var>TEXT</var></span></kbd></td>
</tr>
<tr><td> </td><td>A comma separated list of custom stack annotations (e.g. '1,3,4,5,6,7').
Annotation list must be same length as sequences.</td></tr>
</tbody>
</table>
</td></tr>
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-M</span>, <span class="option">--yaxis <var>UNIT</var></span></kbd></td>
</tr>
<tr><td> </td><td>Height of yaxis in units. (Default: Maximum value with uninformative prior.)</td></tr>
</tbody>
</table>
<p>-Y, --show-yaxis YES/NO Display entropy scale along y-axis? (default: True)</p>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-y</span>, <span class="option">--ylabel <var>TEXT</var></span></kbd></td>
</tr>
<tr><td> </td><td>Y-axis label (default depends on plot type and units)</td></tr>
</tbody>
</table>
<p>-E, --show-ends YES/NO Label the ends of the sequence? (default: False)</p>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-P</span>, <span class="option">--fineprint <var>TEXT</var></span></kbd></td>
</tr>
<tr><td> </td><td><p class="first">The fine print (default: heatlogo version)</p>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">--ticmarks <var>NUMBER</var></span></kbd></td>
</tr>
<tr><td> </td><td>Distance between ticmarks (default: 1.0)</td></tr>
</tbody>
</table>
<p>--errorbars YES/NO Display error bars? (default: True)</p>
<p class="last">--reverse-stacks YES/NO Draw stacks with largest letters on top? (default: True)</p>
</td></tr>
</tbody>
</table>
</blockquote>
</div>
<div class="section" id="advanced-format-options">
<h2>Advanced Format Options</h2>
<p>These options provide fine control over the display of the sequence logo.</p>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">-k</span>, <span class="option">--stack-width <var>POINTS</var></span></kbd></td>
</tr>
<tr><td> </td><td><p class="first">Width of a logo stack (default: 10.8)</p>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">--aspect-ratio <var>POINTS</var></span></kbd></td>
</tr>
<tr><td> </td><td>Ratio of stack height to width (default: 5)</td></tr>
</tbody>
</table>
<p>--box YES/NO Draw boxes around symbols? (default: no)</p>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group" colspan="2">
<kbd><span class="option">--resolution <var>DPI</var></span></kbd></td>
</tr>
<tr><td> </td><td>Bitmap resolution in dots per inch (DPI) (Default: 96 DPI, except
png_print, 600 DPI). Low resolution bitmaps (DPI<300) are antialiased.</td></tr>
</tbody>
</table>
<dl class="last docutils">
<dt>--scale-width YES/NO Scale the visible stack width by the fraction of symbols in the column?</dt>
<dd>(i.e. columns with many gaps of unknowns are narrow.) (Default: yes)</dd>
</dl>
</td></tr>
</tbody>
</table>
</blockquote>
</div>
<div class="section" id="heatlogo-server">
<h2>HeatLogo Server</h2>
<p>Run a standalone webserver on a local port.</p>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group">
<kbd><span class="option">--serve</span></kbd></td>
<td>Start a standalone HeatLogo server for creating sequence logos.</td></tr>
</tbody>
</table>
<p class="attribution">—port PORT Listen to this local port. (Default: 8080)</p>
</blockquote>
</div>
</div>
<div class="section" id="examples">
<h1>Examples</h1>
<p>For help on the command line interface, type:</p>
<pre class="literal-block">
$ ./heatlogo --help
</pre>
<p>To build a simple logo, execute:</p>
<pre class="literal-block">
$ ./heatlogo < seqs.fa > logo.eps
</pre>
<p>If the input data is codon, type:</p>
<pre class="literal-block">
$ ./heatlogo --sequence-type 'codon' < seqs.fa > logo.eps
</pre>
<p>HeatLogo takes into account expected composition of sequences using the following commands.</p>
<ul>
<li><p class="first">String (for DNA, RNA, protein, and codon):</p>
<pre class="literal-block">
$ ./heatlogo --composition ['auto'| 'equiprobable'|'none'] < seqs.fa > logo.eps
</pre>
</li>
<li><p class="first">Explicit distribution of symbols (for DNA, RNA, protein, and codon):</p>
<pre class="literal-block">
$ ./heatlogo --composition "{'A':30, 'C':20, 'G':20, 'T':30}" < seqs.fa > logo.eps
</pre>
</li>
<li><p class="first">CG percentage (only applicable for DNA or RNA):</p>
<pre class="literal-block">
$ ./heatlogo --composition 40% < seqs.fa > logo.eps
</pre>
</li>
<li><p class="first">Tab-delimited file containing each symbol and its composition (for DNA, RNA, protein, and codon):</p>
<pre class="literal-block">
$ ./heatlogo --composition COMPOSITON_FILENAME < seqs.fa > logo.eps
</pre>
<ul>
<li><p class="first">Note: tab-delimited file format</p>
<table border="1" class="docutils">
<colgroup>
<col width="29%" />
<col width="31%" />
<col width="40%" />
</colgroup>
<thead valign="bottom">
<tr><th class="head">DNA or RNA</th>
<th class="head">protein</th>
<th class="head">codon</th>
</tr>
</thead>
<tbody valign="top">
<tr><td>A 24.3</td>
<td>A 13.8</td>
<td>AAA 0.080</td>
</tr>
<tr><td>T 24.3</td>
<td>C 12.1</td>
<td>AAC 0.018</td>
</tr>
<tr><td>G 25.7</td>
<td>D 3.4</td>
<td>AAG 0.409</td>
</tr>
<tr><td>C 25.7</td>
<td>E 8.9 ...</td>
<td>AAT 0.004 ...</td>
</tr>
<tr><td>(4 lines)</td>
<td>(20 lines)</td>
<td>(64 lines)</td>
</tr>
</tbody>
</table>
</li>
</ul>
</li>
</ul>
<p>For calculating statistical significance of each amino acid,
specify a statistical test as follows:</p>
<pre class="literal-block">
$ ./heatlogo --stats-test 'binomial' < seqs.fa > logo.eps
</pre>
<p>If there is negative or paired dataset against the input, HeatLogo computes P-values
by comparing each column of the input with the column of the negative or paired dataset:</p>
<pre class="literal-block">
$ ./heatlogo --second-data FILENAME < seqs.fa > logo.eps
</pre>
<p>Heatmap schemes implemented in HeatLogo can be changed with the following option:</p>
<pre class="literal-block">
$ ./heatlogo --heat-scheme 'red-blue' < seq.fa > logo.eps
</pre>
<p>To generate position weight matrices of P-values and log-odds ratios, type:</p>
<pre class="literal-block">
$ ./heatlogo --pwm-pval FILENAME --pwm-prob FILENAME < seqs.fa > logo.eps
</pre>
<p>HeatLogo also generates sequence logos with usual color schemes by turning off
the heatmap mode:</p>
<pre class="literal-block">
$ ./heatlogo --color-scheme 'base pairing' < seqs.fa > logo.eps
</pre>
</div>
<div class="section" id="color-schemes">
<h1>Color Schemes</h1>
<p>Color schemes (i.e. color schemes which are not heatmap mode) of usual
sequence logos are listed as follows.</p>
<div class="section" id="amino-acids">
<h2>Amino Acids</h2>
<p>All color schemes for amino acids are based on their physicochemical properties.</p>
<ul class="simple">
<li>Hydrophobicity</li>
</ul>
<table border="1" class="docutils">
<colgroup>
<col width="41%" />
<col width="41%" />
<col width="17%" />
</colgroup>
<thead valign="bottom">
<tr><th class="head">Physicochemical prop.</th>
<th class="head">Amino acid</th>
<th class="head">Colors</th>
</tr>
</thead>
<tbody valign="top">
<tr><td>Hydrophilic</td>
<td>R, K, D, E, N, Q</td>
<td>blue</td>
</tr>
<tr><td>Neutral</td>
<td>S, G, H, T, A, P</td>
<td>green</td>
</tr>
<tr><td>Hydrophobic</td>
<td>Y, V, M, C, L, F, I, W</td>
<td>black</td>
</tr>
</tbody>
</table>
<ul class="simple">
<li>Chemistry</li>
</ul>
<table border="1" class="docutils">
<colgroup>
<col width="41%" />
<col width="41%" />
<col width="17%" />
</colgroup>
<thead valign="bottom">
<tr><th class="head">Physicochemical prop.</th>
<th class="head">Amino acid</th>
<th class="head">Colors</th>
</tr>
</thead>
<tbody valign="top">
<tr><td>Polar</td>
<td>G, S, T, Y, C</td>
<td>green</td>
</tr>
<tr><td>Neutral</td>
<td>N, Q</td>
<td>purple</td>
</tr>
<tr><td>Basic</td>
<td>K, R, H</td>
<td>blue</td>
</tr>
<tr><td>Acidic</td>
<td>D, E</td>
<td>red</td>
</tr>
<tr><td>Hydrophobic</td>
<td>P, A, W, F, L, I, M, V</td>
<td>black</td>
</tr>
</tbody>
</table>
<ul class="simple">
<li>Charge</li>
</ul>
<table border="1" class="docutils">
<colgroup>
<col width="50%" />
<col width="29%" />
<col width="21%" />
</colgroup>
<thead valign="bottom">
<tr><th class="head">Physicochemical prop.</th>
<th class="head">Amino acid</th>
<th class="head">Colors</th>
</tr>
</thead>
<tbody valign="top">
<tr><td>Positive</td>
<td>K, R, H</td>
<td>blue</td>
</tr>
<tr><td>Negative</td>
<td>D, E</td>
<td>red</td>
</tr>
</tbody>
</table>
</div>
<div class="section" id="codons">
<h2>Codons</h2>
<p>The color scheme is based on physicochemical properties of amino acids
encoded by codons according to the standard genetic code table.</p>
<table border="1" class="docutils">
<colgroup>
<col width="37%" />
<col width="22%" />
<col width="42%" />
</colgroup>
<thead valign="bottom">
<tr><th class="head">Physicochemical prop.</th>
<th class="head">Amino acid</th>
<th class="head">Colors</th>
</tr>
</thead>
<tbody valign="top">
<tr><td>Polar positive</td>
<td>H, K, R</td>
<td>light blue</td>
</tr>
<tr><td>Polar negative</td>
<td>D, E</td>
<td>red</td>
</tr>
<tr><td>Polar neutral</td>
<td>S, T, N, Q</td>
<td>green</td>
</tr>
<tr><td>Non-polar aliphatic</td>
<td>A, V, L, I</td>
<td>blue</td>
</tr>