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author grau
date Wed, 13 Nov 2013 04:25:23 -0500
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1 <html>
2 <head>
3 <title>
4 Summary of Dimont results</title>
5 <style type="text/css">body{font-family:sans-serif;font-size:10pt}
6 table{font-size:10pt;border-spacing:0px}
7 th{font-weight:bold}
8 div.head{font-size:15px;line-height:24px;padding:5px 10px;background:#ebd9b2;border-bottom:solid #d8b365 1px;font-weight:bold}
9 div.comment{color:grey}
10 h2{text-align:center}</style></head>
11 <h2><title>
12 Summary of Dimont results</title>
13 </h2><body>
14 <div class="head">
15 Motif 1</div>
16 <br /><img src="Motif_0.png" alt="Motif 1" width="749" height="529"/><div class="comment">
17 Sequence logo of motif 1</div>
18 <br /><div class="head">
19 Motif 1 (rc)</div>
20 <br /><img src="Motif_(rc)1.png" alt="Motif 1 (rc)" width="749" height="529"/><div class="comment">
21 Sequence logo of the reverse complement of motif 1</div>
22 <br /><div class="head">
23 Motif 2</div>
24 <br /><img src="Motif_2.png" alt="Motif 2" width="749" height="529"/><div class="comment">
25 Sequence logo of motif 2</div>
26 <br /><div class="head">
27 Motif 2 (rc)</div>
28 <br /><img src="Motif_(rc)3.png" alt="Motif 2 (rc)" width="749" height="529"/><div class="comment">
29 Sequence logo of the reverse complement of motif 2</div>
30 <br /><div class="head">
31 Description of columns of binding site output (see history)</div>
32 <br /><div>
33 <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>
34 <div class="comment">
35 You can download the predictions for the motifs discovered as tab-separated file from the history.</div>
36 <br /><div class="head">
37 Protocol</div>
38 <br /><div>
39 -----------------------------------------<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>
40 <div class="comment">
41 The protocol of this Dimont run</div>
42 <br /></body>
43 </html>
44