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<a href="Bio.SeqUtils-module.html">Package SeqUtils</a> ::
Module MeltingTemp
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<h1 class="epydoc">Source Code for <a href="Bio.SeqUtils.MeltingTemp-module.html">Module Bio.SeqUtils.MeltingTemp</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">math</tt> </tt>
<a name="Tm_staluc"></a><div id="Tm_staluc-def"><a name="L2"></a><tt class="py-lineno"> 2</tt> <a class="py-toggle" href="#" id="Tm_staluc-toggle" onclick="return toggle('Tm_staluc');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.MeltingTemp-module.html#Tm_staluc">Tm_staluc</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">,</tt><tt class="py-param">dnac</tt><tt class="py-op">=</tt><tt class="py-number">50</tt><tt class="py-op">,</tt><tt class="py-param">saltc</tt><tt class="py-op">=</tt><tt class="py-number">50</tt><tt class="py-op">,</tt><tt class="py-param">rna</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tm_staluc-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Tm_staluc-expanded"><a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns DNA/DNA tm using nearest neighbor thermodynamics.</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring"> dnac is DNA concentration [nM]</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring"> saltc is salt concentration [mM].</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"> rna=0 is for DNA/DNA (default), for RNA, rna should be 1.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"> Sebastian Bassi <sbassi@genesdigitales.com>"""</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> <tt class="py-comment">#Credits: </tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Main author: Sebastian Bassi <sbassi@genesdigitales.com></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Overcount function: Greg Singer <singerg@tcd.ie></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Based on the work of Nicolas Le Novere <lenov@ebi.ac.uk> Bioinformatics.</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#17:1226-1227(2001)</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-comment">#This function returns better results than EMBOSS DAN because it uses</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#updated thermodynamics values and takes into account inicialization</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#parameters from the work of SantaLucia (1998).</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-comment">#Things to do:</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#+Detect complementary sequences. Change K according to result.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#+Add support for heteroduplex (see Sugimoto et al. 1995).</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#+Correction for Mg2+. Now supports only monovalent ions.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#+Put thermodinamics table in a external file for users to change at will</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#+Add support for danglings ends (see Le Novele. 2001) and mismatches.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-name">dh</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> <tt class="py-comment">#DeltaH. Enthalpy</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt id="link-0" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.ds()=Bio.Sequencing.Ace._RecordConsumer-class.html#ds,Class Bio.Sequencing.Ace.ds=Bio.Sequencing.Ace.ds-class.html"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-0', 'ds', 'link-0');">ds</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> <tt class="py-comment">#deltaS Entropy</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">tercorr</tt><tt class="py-op">(</tt><tt class="py-param">stri</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">deltah</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">deltas</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rna</tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-comment">#DNA/DNA</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Allawi and SantaLucia (1997). Biochemistry 36 : 10581-10594</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'G'</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'C'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">deltah</tt><tt class="py-op">=</tt><tt class="py-name">deltah</tt><tt class="py-op">-</tt><tt class="py-number">0.1</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">deltas</tt><tt class="py-op">=</tt><tt class="py-name">deltas</tt><tt class="py-op">+</tt><tt class="py-number">2.8</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'A'</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'T'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">deltah</tt><tt class="py-op">=</tt><tt class="py-name">deltah</tt><tt class="py-op">-</tt><tt class="py-number">2.3</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">deltas</tt><tt class="py-op">=</tt><tt class="py-name">deltas</tt><tt class="py-op">-</tt><tt class="py-number">4.1</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'G'</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'C'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">deltah</tt><tt class="py-op">=</tt><tt class="py-name">deltah</tt><tt class="py-op">-</tt><tt class="py-number">0.1</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-name">deltas</tt><tt class="py-op">=</tt><tt class="py-name">deltas</tt><tt class="py-op">+</tt><tt class="py-number">2.8</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'A'</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'T'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-name">deltah</tt><tt class="py-op">=</tt><tt class="py-name">deltah</tt><tt class="py-op">-</tt><tt class="py-number">2.3</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">deltas</tt><tt class="py-op">=</tt><tt class="py-name">deltas</tt><tt class="py-op">-</tt><tt class="py-number">4.1</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">dhL</tt><tt class="py-op">=</tt><tt class="py-name">dh</tt><tt class="py-op">+</tt><tt class="py-name">deltah</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">dsL</tt><tt class="py-op">=</tt><tt id="link-1" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-1', 'ds', 'link-0');">ds</a></tt><tt class="py-op">+</tt><tt class="py-name">deltas</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">dsL</tt><tt class="py-op">,</tt><tt class="py-name">dhL</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">rna</tt><tt class="py-op">==</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-comment">#RNA</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'G'</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'C'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">deltah</tt><tt class="py-op">=</tt><tt class="py-name">deltah</tt><tt class="py-op">-</tt><tt class="py-number">3.61</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-name">deltas</tt><tt class="py-op">=</tt><tt class="py-name">deltas</tt><tt class="py-op">-</tt><tt class="py-number">1.5</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'A'</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'T'</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'U'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">deltah</tt><tt class="py-op">=</tt><tt class="py-name">deltah</tt><tt class="py-op">-</tt><tt class="py-number">3.72</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">deltas</tt><tt class="py-op">=</tt><tt class="py-name">deltas</tt><tt class="py-op">+</tt><tt class="py-number">10.5</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'G'</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'C'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">deltah</tt><tt class="py-op">=</tt><tt class="py-name">deltah</tt><tt class="py-op">-</tt><tt class="py-number">3.61</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">deltas</tt><tt class="py-op">=</tt><tt class="py-name">deltas</tt><tt class="py-op">-</tt><tt class="py-number">1.5</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'A'</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'T'</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">stri</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'U'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">deltah</tt><tt class="py-op">=</tt><tt class="py-name">deltah</tt><tt class="py-op">-</tt><tt class="py-number">3.72</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">deltas</tt><tt class="py-op">=</tt><tt class="py-name">deltas</tt><tt class="py-op">+</tt><tt class="py-number">10.5</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">dhL</tt><tt class="py-op">=</tt><tt class="py-name">dh</tt><tt class="py-op">+</tt><tt class="py-name">deltah</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">dsL</tt><tt class="py-op">=</tt><tt id="link-2" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-2', 'ds', 'link-0');">ds</a></tt><tt class="py-op">+</tt><tt class="py-name">deltas</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-comment"># print "delta h=",dhL</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">dsL</tt><tt class="py-op">,</tt><tt class="py-name">dhL</tt> </tt>
</div><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">overcount</tt><tt class="py-op">(</tt><tt class="py-param">st</tt><tt class="py-op">,</tt><tt class="py-param">p</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns how many p are on st, works even for overlapping"""</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">ocu</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt id="link-3" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-3', 'x', 'link-3');">x</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt id="link-4" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-4', 'i', 'link-4');">i</a></tt><tt class="py-op">=</tt><tt class="py-name">st</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-5', 'index', 'link-5');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt id="link-6" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-6', 'x', 'link-3');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">ocu</tt><tt class="py-op">=</tt><tt class="py-name">ocu</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt id="link-7" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-7', 'x', 'link-3');">x</a></tt><tt class="py-op">=</tt><tt id="link-8" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-8', 'i', 'link-4');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ocu</tt> </tt>
</div><a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">R</tt><tt class="py-op">=</tt><tt class="py-number">1.987</tt> <tt class="py-comment"># universal gas constant in Cal/degrees C*Mol</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">sup</tt><tt class="py-op">=</tt><tt id="link-9" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-9', 's', 'link-9');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">vsTC</tt><tt class="py-op">,</tt><tt class="py-name">vh</tt><tt class="py-op">=</tt><tt class="py-name">tercorr</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">vs</tt><tt class="py-op">=</tt><tt class="py-name">vsTC</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">k</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">dnac</tt><tt class="py-op">/</tt><tt class="py-number">4.0</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">1e-9</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-comment">#With complementary check on, the 4.0 should be changed to a variable.</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rna</tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-comment">#DNA/DNA</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Allawi and SantaLucia (1997). Biochemistry 36 : 10581-10594</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">vh</tt><tt class="py-op">=</tt><tt class="py-name">vh</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">7.9</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">7.9</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">7.2</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">7.2</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">8.5</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">8.5</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">8.4</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">8.4</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">vh</tt><tt class="py-op">=</tt><tt class="py-name">vh</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">7.8</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">7.8</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">8.2</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">8.2</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">vh</tt><tt class="py-op">=</tt><tt class="py-name">vh</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">10.6</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">9.8</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">8</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">8</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">vs</tt><tt class="py-op">=</tt><tt class="py-name">vs</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">22.2</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">22.2</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">20.4</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">21.3</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">vs</tt><tt class="py-op">=</tt><tt class="py-name">vs</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">22.7</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">22.7</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">22.4</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">22.4</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">vs</tt><tt class="py-op">=</tt><tt class="py-name">vs</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">21.0</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">21.0</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">22.2</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">22.2</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">vs</tt><tt class="py-op">=</tt><tt class="py-name">vs</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">27.2</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">24.4</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">19.9</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">19.9</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt id="link-10" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-10', 'ds', 'link-0');">ds</a></tt><tt class="py-op">=</tt><tt class="py-name">vs</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">dh</tt><tt class="py-op">=</tt><tt class="py-name">vh</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-comment">#RNA/RNA hybridisation of Xia et al (1998)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Biochemistry 37: 14719-14735 </tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">vh</tt><tt class="py-op">=</tt><tt class="py-name">vh</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">6.82</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">6.6</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">9.38</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">7.69</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">10.44</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">10.5</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">11.4</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">10.2</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">vh</tt><tt class="py-op">=</tt><tt class="py-name">vh</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">10.48</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">7.6</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">12.44</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">13.3</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">vh</tt><tt class="py-op">=</tt><tt class="py-name">vh</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">10.64</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">14.88</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">13.39</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">12.2</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">vs</tt><tt class="py-op">=</tt><tt class="py-name">vs</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">19.0</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">18.4</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">26.7</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">20.5</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">vs</tt><tt class="py-op">=</tt><tt class="py-name">vs</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">26.9</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">27.8</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">29.5</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">26.2</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">vs</tt><tt class="py-op">=</tt><tt class="py-name">vs</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">27.1</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"AG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">19.2</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GA"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">32.5</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"TC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">35.5</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">vs</tt><tt class="py-op">=</tt><tt class="py-name">vs</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">26.7</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">36.9</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"GG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">32.7</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">overcount</tt><tt class="py-op">(</tt><tt class="py-name">sup</tt><tt class="py-op">,</tt><tt class="py-string">"CC"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">29.7</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt id="link-11" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-11', 'ds', 'link-0');">ds</a></tt><tt class="py-op">=</tt><tt class="py-name">vs</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">dh</tt><tt class="py-op">=</tt><tt class="py-name">vh</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt id="link-12" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-12', 'ds', 'link-0');">ds</a></tt><tt class="py-op">=</tt><tt id="link-13" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-13', 'ds', 'link-0');">ds</a></tt><tt class="py-op">-</tt><tt class="py-number">0.368</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-14', 's', 'link-9');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Variable Bio.Affy.CelFile.log=Bio.Affy.CelFile-module.html#log,Variable Bio.LogisticRegression.log=Bio.LogisticRegression-module.html#log,Variable Bio.MarkovModel.log=Bio.MarkovModel-module.html#log,Variable Bio.MaxEntropy.log=Bio.MaxEntropy-module.html#log,Variable Bio.NaiveBayes.log=Bio.NaiveBayes-module.html#log,Variable Bio.Statistics.lowess.log=Bio.Statistics.lowess-module.html#log,Variable Bio.distance.log=Bio.distance-module.html#log,Variable Bio.kNN.log=Bio.kNN-module.html#log"><a title="Bio.Affy.CelFile.log
Bio.LogisticRegression.log
Bio.MarkovModel.log
Bio.MaxEntropy.log
Bio.NaiveBayes.log
Bio.Statistics.lowess.log
Bio.distance.log
Bio.kNN.log" class="py-name" href="#" onclick="return doclink('link-15', 'log', 'link-15');">log</a></tt><tt class="py-op">(</tt><tt class="py-name">saltc</tt><tt class="py-op">/</tt><tt class="py-number">1e3</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-name">tm</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-number">1000</tt><tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-name">dh</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt id="link-16" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-16', 'ds', 'link-0');">ds</a></tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">R</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.Affy.CelFile.log
Bio.LogisticRegression.log
Bio.MarkovModel.log
Bio.MaxEntropy.log
Bio.NaiveBayes.log
Bio.Statistics.lowess.log
Bio.distance.log
Bio.kNN.log" class="py-name" href="#" onclick="return doclink('link-17', 'log', 'link-15');">log</a></tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">273.15</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-comment"># print "ds="+str(ds)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># print "dh="+str(dh)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">tm</tt> </tt>
</div><a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> </tt><script type="text/javascript">
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