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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqUtils-module.html">Package SeqUtils</a> ::
Module CodonUsageIndices
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<h1 class="epydoc">Source Code for <a href="Bio.SeqUtils.CodonUsageIndices-module.html">Module Bio.SeqUtils.CodonUsageIndices</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright Yair Benita Y.Benita@pharm.uu.nl</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Biopython (http://biopython.org) license applies</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># sharp Ecoli index for codon adaption index.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># from Sharp & Li, Nucleic Acids Res. 1987</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-0" class="py-name" targets="Variable Bio.SeqUtils.CodonUsageIndices.SharpEcoliIndex=Bio.SeqUtils.CodonUsageIndices-module.html#SharpEcoliIndex"><a title="Bio.SeqUtils.CodonUsageIndices.SharpEcoliIndex" class="py-name" href="#" onclick="return doclink('link-0', 'SharpEcoliIndex', 'link-0');">SharpEcoliIndex</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-string">'GCA'</tt><tt class="py-op">:</tt><tt class="py-number">0.586</tt><tt class="py-op">,</tt> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt><tt class="py-number">0.122</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt><tt class="py-number">0.424</tt><tt class="py-op">,</tt> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt><tt class="py-number">0.004</tt><tt class="py-op">,</tt> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt><tt class="py-number">0.002</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt><tt class="py-number">0.004</tt><tt class="py-op">,</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-string">'CGC'</tt><tt class="py-op">:</tt><tt class="py-number">0.356</tt><tt class="py-op">,</tt> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt><tt class="py-number">0.004</tt><tt class="py-op">,</tt> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt><tt class="py-number">0.051</tt><tt class="py-op">,</tt> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt><tt class="py-number">0.434</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-string">'TGT'</tt><tt class="py-op">:</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt><tt class="py-number">0.124</tt><tt class="py-op">,</tt> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt><tt class="py-number">0.259</tt><tt class="py-op">,</tt> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt><tt class="py-number">0.01</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt><tt class="py-number">0.724</tt><tt class="py-op">,</tt> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt><tt class="py-number">0.019</tt><tt class="py-op">,</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-string">'GGT'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt><tt class="py-number">0.291</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt><tt class="py-number">0.003</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt><tt class="py-number">0.185</tt><tt class="py-op">,</tt> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt><tt class="py-number">0.007</tt><tt class="py-op">,</tt> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt><tt class="py-number">0.037</tt><tt class="py-op">,</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-string">'CTG'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt><tt class="py-number">0.042</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt><tt class="py-number">0.02</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt><tt class="py-number">0.02</tt><tt class="py-op">,</tt> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt><tt class="py-number">0.253</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'TTT'</tt><tt class="py-op">:</tt><tt class="py-number">0.296</tt><tt class="py-op">,</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-string">'CCA'</tt><tt class="py-op">:</tt><tt class="py-number">0.135</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt><tt class="py-number">0.012</tt><tt class="py-op">,</tt> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt><tt class="py-number">0.07</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt><tt class="py-number">0.41</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt><tt class="py-number">0.085</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt><tt class="py-number">0.077</tt><tt class="py-op">,</tt> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt><tt class="py-number">0.744</tt><tt class="py-op">,</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-string">'TCG'</tt><tt class="py-op">:</tt><tt class="py-number">0.017</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt><tt class="py-number">0.076</tt><tt class="py-op">,</tt> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-string">'ACG'</tt><tt class="py-op">:</tt><tt class="py-number">0.099</tt><tt class="py-op">,</tt> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt><tt class="py-number">0.965</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt><tt class="py-number">0.239</tt><tt class="py-op">,</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-string">'GTA'</tt><tt class="py-op">:</tt><tt class="py-number">0.495</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt><tt class="py-number">0.066</tt><tt class="py-op">,</tt><tt class="py-string">'GTG'</tt><tt class="py-op">:</tt><tt class="py-number">0.221</tt><tt class="py-op">,</tt> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">}</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> </tt><script type="text/javascript">
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