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date Tue, 12 Nov 2013 13:01:21 -0500
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Summary of Dimont results</title>
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Summary of Dimont results</title>
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Motif 1</div>
<br /><img src="Motif_0.png" alt="Motif 1" width="749" height="529"/><div class="comment">
Sequence logo of motif 1</div>
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Motif 1 (rc)</div>
<br /><img src="Motif_(rc)1.png" alt="Motif 1 (rc)" width="749" height="529"/><div class="comment">
Sequence logo of the reverse complement of motif 1</div>
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Motif 2</div>
<br /><img src="Motif_2.png" alt="Motif 2" width="749" height="529"/><div class="comment">
Sequence logo of motif 2</div>
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Motif 2 (rc)</div>
<br /><img src="Motif_(rc)3.png" alt="Motif 2 (rc)" width="749" height="529"/><div class="comment">
Sequence logo of the reverse complement of motif 2</div>
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Description of columns of binding site output (see history)</div>
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<table border="1"><tr><th>Column</th><th>Description</th></tr><tr><td>Sequence index</td><td>The index of the sequence</td></tr><tr><td>Position</td><td>The start position of predicted binding site (BS) within the sequence</td></tr><tr><td>Strand</td><td>The strand of the predicted BS</td></tr><tr><td>p-value</td><td>The p-value of the predicted BS</td></tr><tr><td>Binding site</td><td>The binding site as in the sequence</td></tr><tr><td>Adjusted binding site</td><td>The binding site in predicted orientation</td></tr><tr><td>Sequence annotation</td><td>The annotation of the original sequence</td></tr></table></div>
<div class="comment">
You can download the predictions for the motifs discovered as tab-separated file from the history.</div>
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Protocol</div>
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-----------------------------------------<br />pre-optimization 0<br />consensus: NNNGGATTAgNNNNN<br />score: -0.295567005150279<br />-----------------------------------------<br />pre-optimization 1<br />consensus: NNNNNNNGCTAATCC<br />score: -0.2968705301682643<br />-----------------------------------------<br />pre-optimization 2<br />consensus: NNNNNNNNNGGATTA<br />score: -0.2998645110489622<br />-----------------------------------------<br />pre-optimization 3<br />consensus: NNNNNNNCTACCTGN<br />score: -0.3087596251574336<br />-----------------------------------------<br />pre-optimization 4<br />consensus: NNNNNNNcTAATCCN<br />score: -0.29644063340606813<br />-----------------------------------------<br />pre-optimization 5<br />consensus: NNNNNNNcTAATCCN<br />score: -0.2966054557344498<br />-----------------------------------------<br />pre-optimization 6<br />consensus: NNNNNNGGATTAgNN<br />score: -0.2960250155204568<br />-----------------------------------------<br />pre-optimization 7<br />consensus: NNNNNNNNGGATTAG<br />score: -0.29700657112246615<br />-----------------------------------------<br />pre-optimization 8<br />consensus: NNNNNNNNGGATTAG<br />score: -0.2968825997973593<br />-----------------------------------------<br />pre-optimization 9<br />consensus: NcTAATCCNNNNNNN<br />score: -0.29658902318223385<br />-----------------------------------------<br />pre-optimization 10<br />consensus: NNNNNcTAATCCNNN<br />score: -0.2956125682458301<br />-----------------------------------------<br />pre-optimization 11<br />consensus: NNNNNNNcTAATCCN<br />score: -0.296571619107918<br />-----------------------------------------<br />pre-optimization 12<br />consensus: NNNNNNNcTAATCCN<br />score: -0.2962341972836779<br />-----------------------------------------<br />pre-optimization 13<br />consensus: NcTAATCCNNNNNNN<br />score: -0.29655816176857164<br />-----------------------------------------<br />pre-optimization 14<br />consensus: NcTAATCCNNNNNNN<br />score: -0.2965258452522728<br />-----------------------------------------<br />pre-optimization 15<br />consensus: NNNNGGATTAgNNNN<br />score: -0.29611726030602253<br />-----------------------------------------<br />pre-optimization 16<br />consensus: NNNNGGATTAgNNNN<br />score: -0.29582934750532014<br />-----------------------------------------<br />pre-optimization 17<br />consensus: NNNNGGATTAgNNNN<br />score: -0.2960919285853769<br />-----------------------------------------<br />pre-optimization 18<br />consensus: NNNNCAGGTAGNNNN<br />score: -0.309349126583713<br />-----------------------------------------<br />pre-optimization 19<br />consensus: NNNNcTAATCCNNNN<br />score: -0.29618438710408135<br />-----------------------------------------<br />added: NNNGGATTAgNNNNN<br />added: NNNNNNNCTACCTGN<br />number of motifs: 2<br />+++++++++++++++++++++++++++++++++++++++++++++++++++<br /><br />finalOpt 0 -----------------------------------------<br />left: 3, right: -5<br />modified motif<br />consensus: GGATTAG<br />+++++++++++++++++++++++++++++++++++++++++++++++++++<br /><br />finalOpt 1 -----------------------------------------<br />left: 7, right: -1<br />modified motif<br />consensus: CTACCTG<br /><br />++++++++++++++++++++++++++++++++++++++++++++++<br /><br /><strong>Motif model 1</strong><br /><p><strong>motif probability:</strong> 0.906</p><p><strong>Probabilities at position 0:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.144</td><td>0.087</td><td>0.725</td><td>0.044</td></tr></table></p><p><strong>Probabilities at position 1:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.040</td><td>0.045</td><td>0.868</td><td>0.047</td></tr></table></p><p><strong>Probabilities at position 2:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.686</td><td>0.188</td><td>0.061</td><td>0.065</td></tr></table></p><p><strong>Probabilities at position 3:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.048</td><td>0.120</td><td>0.052</td><td>0.781</td></tr></table></p><p><strong>Probabilities at position 4:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.055</td><td>0.130</td><td>0.040</td><td>0.776</td></tr></table></p><p><strong>Probabilities at position 5:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.711</td><td>0.067</td><td>0.057</td><td>0.165</td></tr></table></p><p><strong>Probabilities at position 6:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.319</td><td>0.080</td><td>0.424</td><td>0.177</td></tr></table></p><br />++++++++++++++++++++++++++++++++++++++++++++++<br /><br /><strong>Motif model 2</strong><br /><p><strong>motif probability:</strong> 0.892</p><p><strong>Probabilities at position 0:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.104</td><td>0.451</td><td>0.177</td><td>0.268</td></tr></table></p><p><strong>Probabilities at position 1:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.063</td><td>0.032</td><td>0.152</td><td>0.753</td></tr></table></p><p><strong>Probabilities at position 2:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.729</td><td>0.063</td><td>0.147</td><td>0.061</td></tr></table></p><p><strong>Probabilities at position 3:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.048</td><td>0.847</td><td>0.061</td><td>0.044</td></tr></table></p><p><strong>Probabilities at position 4:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.045</td><td>0.827</td><td>0.078</td><td>0.051</td></tr></table></p><p><strong>Probabilities at position 5:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.046</td><td>0.078</td><td>0.105</td><td>0.771</td></tr></table></p><p><strong>Probabilities at position 6:<strong><br/><table border="1"><tr><th>A</th><th>C</th><th>G</th><th>T</th></tr><tr><td>0.242</td><td>0.081</td><td>0.603</td><td>0.074</td></tr></table></p></div>
<div class="comment">
The protocol of this Dimont run</div>
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