imported>Gydbwiki: CAARD mag

2009-05-08T09:50:16Z

CAARD mag

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{{CAARD
|pin_output=
(Cer4:0.227252,(Gulliver:0.804526,(Mag:0.655884,SURL:0.646649)N3:0.161094)N2:0.171023,(Cigr-1:1.152764,(Cer5:0.235950,Cer6:0.207646) N5:0.142782)N4:0.016193);

|fin_output=

<table class="tabdata">
<tr class="grey">
<td>Name</td>
<td>Father</td>
<td>Distance to father</td>
<td>Sons</td>
<tr>
<tr><td>Cer4</td><td>N1</td><td>0.227252</td><td>-</td></tr><tr><td>Gulliver</td><td>N2</td><td>0.804526</td><td>-</td></tr><tr><td>Mag</td><td>N3</td><td>0.655884</td><td>-</td></tr><tr><td>SURL</td><td>N3</td><td>0.646649</td><td>-</td></tr><tr><td>Cigr-1</td><td>N4</td><td>1.15276</td><td>-</td></tr><tr><td>Cer5</td><td>N5</td><td>0.23595</td><td>-</td></tr><tr><td>Cer6</td><td>N5</td><td>0.207646</td><td>-</td></tr><tr><td>N1</td><td>root!</td><td>-</td><td>Cer4 N2 N4</td></tr><tr><td>N2</td><td>N1</td><td>0.171023</td><td>Gulliver N3</td></tr><tr><td>N3</td><td>N2</td><td>0.161094</td><td>Mag SURL</td></tr><tr><td>N4</td><td>N1</td><td>0.016193</td><td>Cigr-1 N5</td></tr><tr><td>N5</td><td>N4</td><td>0.142782</td><td>Cer5 Cer6</td></tr>
</table>

|jpf_output=
<table class="tabdata">
<tr class="grey">
<td>Position</td>
<td>Joint probability</td>
<td>Position</td>
<td>Joint probability</td>
<td>Position</td>
<td>Joint probability</td>
<td>Position</td>
<td>Joint probability</td>
<tr>
<tr class="text"><td>0</td><td>1.32988e-005</td><td>25</td><td>2.11241e-006</td><td>50</td><td>1.34827e-007</td><td>75</td><td>9.07489e-011</td></tr><tr class="text"><td>1</td><td>0.000762449</td><td>26</td><td>0.000166752</td><td>51</td><td>4.86902e-005</td><td>76</td><td>3.82289e-008</td></tr><tr class="text"><td>2</td><td>0.000109251</td><td>27</td><td>0.0199432</td><td>52</td><td>4.06078e-010</td><td>77</td><td>8.33098e-007</td></tr><tr class="text"><td>3</td><td>3.50389e-005</td><td>28</td><td>0.0220334</td><td>53</td><td>8.12997e-009</td><td>78</td><td>0.000361318</td></tr><tr class="text"><td>4</td><td>0.0123056</td><td>29</td><td>8.01234e-013</td><td>54</td><td>9.12806e-010</td><td>79</td><td>0.000854334</td></tr><tr class="text"><td>5</td><td>4.721e-005</td><td>30</td><td>2.29719e-010</td><td>55</td><td>7.44592e-007</td><td>80</td><td>0.000147356</td></tr><tr class="text"><td>6</td><td>1.47045e-011</td><td>31</td><td>0.000175138</td><td>56</td><td>7.83865e-006</td><td>81</td><td>0.00460652</td></tr><tr class="text"><td>7</td><td>2.42989e-007</td><td>32</td><td>1.53924e-007</td><td>57</td><td>0.000189816</td><td>82</td><td>1.51198e-010</td></tr><tr class="text"><td>8</td><td>1.93624e-005</td><td>33</td><td>1.10374e-010</td><td>58</td><td>1.14953e-006</td><td>83</td><td>6.66742e-009</td></tr><tr class="text"><td>9</td><td>2.2472e-007</td><td>34</td><td>8.28717e-011</td><td>59</td><td>7.28578e-005</td><td>84</td><td>0.0122317</td></tr><tr class="text"><td>10</td><td>2.24517e-007</td><td>35</td><td>4.69345e-014</td><td>60</td><td>8.07759e-010</td><td>85</td><td>6.64523e-007</td></tr><tr class="text"><td>11</td><td>3.43742e-007</td><td>36</td><td>1.93332e-008</td><td>61</td><td>3.92755e-009</td><td>86</td><td>4.47863e-008</td></tr><tr class="text"><td>12</td><td>1.29732e-010</td><td>37</td><td>0.0223989</td><td>62</td><td>3.1221e-008</td><td>87</td><td>5.83828e-006</td></tr><tr class="text"><td>13</td><td>2.58159e-011</td><td>38</td><td>1.24e-006</td><td>63</td><td>1.05636e-009</td><td>88</td><td>1.01244e-010</td></tr><tr class="text"><td>14</td><td>6.8833e-010</td><td>39</td><td>1.96873e-006</td><td>64</td><td>1.15034e-009</td><td>89</td><td>3.32357e-009</td></tr><tr class="text"><td>15</td><td>1.75258e-007</td><td>40</td><td>2.56951e-006</td><td>65</td><td>0.0115757</td><td>90</td><td>6.28565e-010</td></tr><tr class="text"><td>16</td><td>2.0513e-009</td><td>41</td><td>1.79752e-007</td><td>66</td><td>8.14125e-011</td><td>91</td><td>2.46668e-007</td></tr><tr class="text"><td>17</td><td>1.35815e-005</td><td>42</td><td>2.9916e-009</td><td>67</td><td>1.16225e-010</td><td>92</td><td>1.99655e-010</td></tr><tr class="text"><td>18</td><td>3.67024e-010</td><td>43</td><td>2.44301e-007</td><td>68</td><td>2.12162e-006</td><td>93</td><td>1.1576e-006</td></tr><tr class="text"><td>19</td><td>1.43795e-006</td><td>44</td><td>1.70486e-009</td><td>69</td><td>0.000523017</td><td>94</td><td>0.00891111</td></tr><tr class="text"><td>20</td><td>2.09857e-005</td><td>45</td><td>7.54047e-008</td><td>70</td><td>3.71239e-009</td><td>95</td><td>3.34396e-006</td></tr><tr class="text"><td>21</td><td>2.87728e-009</td><td>46</td><td>1.50341e-008</td><td>71</td><td>3.33228e-008</td><td>96</td><td>3.97525e-011</td></tr><tr class="text"><td>22</td><td>9.58635e-008</td><td>47</td><td>0.00460652</td><td>72</td><td>1.96354e-005</td><td>97</td><td>6.19115e-008</td></tr><tr class="text"><td>23</td><td>3.54282e-009</td><td>48</td><td>1.83773e-007</td><td>73</td><td>0.00201758</td><td> </td><td> </td></tr><tr class="text"><td>24</td><td>1.94628e-006</td><td>49</td><td>4.10256e-007</td><td>74</td><td>8.20494e-007</td><td> </td><td> </td></tr><tr><td colspan="7" class="grey right">Total log likelihood of joint reconstruction: </td><td class="grey">-1487.94</td></tr>
</table>

|jrof_output=
<align id="mag" folder="jrof"></align>

|mpf_output=
<table class="tabdata">
<tr class="grey">
<td>Position</td>
<td>Joint probability</td>
<td>Position</td>
<td>Joint probability</td>
<td>Position</td>
<td>Joint probability</td>
<td>Position</td>
<td>Joint probability</td>
<tr>
<tr class="text"><td>0</td><td>3.33802e-005</td><td>25</td><td>3.10537e-006</td><td>50</td><td>3.44842e-007</td><td>75</td><td>9.23118e-010</td></tr><tr class="text"><td>1</td><td>0.000771506</td><td>26</td><td>0.000286987</td><td>51</td><td>5.68879e-005</td><td>76</td><td>5.20718e-008</td></tr><tr class="text"><td>2</td><td>0.000110463</td><td>27</td><td>0.076748</td><td>52</td><td>8.25433e-010</td><td>77</td><td>9.25217e-007</td></tr><tr class="text"><td>3</td><td>3.51214e-005</td><td>28</td><td>0.058676</td><td>53</td><td>4.47845e-008</td><td>78</td><td>0.00159519</td></tr><tr class="text"><td>4</td><td>0.076748</td><td>29</td><td>6.7415e-012</td><td>54</td><td>1.98406e-009</td><td>79</td><td>0.000857662</td></tr><tr class="text"><td>5</td><td>5.21007e-005</td><td>30</td><td>8.5022e-010</td><td>55</td><td>1.00672e-006</td><td>80</td><td>0.000153298</td></tr><tr class="text"><td>6</td><td>7.70027e-011</td><td>31</td><td>0.000243101</td><td>56</td><td>7.95964e-006</td><td>81</td><td>0.00461024</td></tr><tr class="text"><td>7</td><td>3.89669e-007</td><td>32</td><td>1.92097e-007</td><td>57</td><td>0.000427039</td><td>82</td><td>4.46751e-010</td></tr><tr class="text"><td>8</td><td>3.43897e-005</td><td>33</td><td>5.18555e-010</td><td>58</td><td>1.33484e-005</td><td>83</td><td>3.80112e-008</td></tr><tr class="text"><td>9</td><td>2.44407e-007</td><td>34</td><td>1.87278e-010</td><td>59</td><td>7.40956e-005</td><td>84</td><td>1</td></tr><tr class="text"><td>10</td><td>5.01827e-007</td><td>35</td><td>1.14334e-012</td><td>60</td><td>1.2564e-009</td><td>85</td><td>6.65409e-007</td></tr><tr class="text"><td>11</td><td>4.25318e-007</td><td>36</td><td>5.64927e-008</td><td>61</td><td>1.72532e-008</td><td>86</td><td>7.18923e-008</td></tr><tr class="text"><td>12</td><td>3.43003e-010</td><td>37</td><td>0.06183</td><td>62</td><td>1.3153e-007</td><td>87</td><td>2.89723e-005</td></tr><tr class="text"><td>13</td><td>1.15152e-010</td><td>38</td><td>1.34986e-006</td><td>63</td><td>2.30279e-009</td><td>88</td><td>6.54461e-010</td></tr><tr class="text"><td>14</td><td>3.14637e-009</td><td>39</td><td>4.13861e-006</td><td>64</td><td>5.63848e-009</td><td>89</td><td>6.41678e-009</td></tr><tr class="text"><td>15</td><td>1.95001e-007</td><td>40</td><td>2.72294e-006</td><td>65</td><td>0.066005</td><td>90</td><td>1.17998e-009</td></tr><tr class="text"><td>16</td><td>9.31313e-009</td><td>41</td><td>3.9614e-007</td><td>66</td><td>5.37916e-010</td><td>91</td><td>7.4016e-007</td></tr><tr class="text"><td>17</td><td>1.39006e-005</td><td>42</td><td>5.00291e-009</td><td>67</td><td>8.36574e-010</td><td>92</td><td>6.74256e-010</td></tr><tr class="text"><td>18</td><td>7.21506e-010</td><td>43</td><td>9.42333e-007</td><td>68</td><td>2.18421e-006</td><td>93</td><td>1.64144e-006</td></tr><tr class="text"><td>19</td><td>2.40196e-006</td><td>44</td><td>7.08827e-009</td><td>69</td><td>0.000539592</td><td>94</td><td>0.053761</td></tr><tr class="text"><td>20</td><td>4.99911e-005</td><td>45</td><td>8.96987e-008</td><td>70</td><td>4.74142e-008</td><td>95</td><td>3.61824e-006</td></tr><tr class="text"><td>21</td><td>6.43375e-009</td><td>46</td><td>2.71808e-008</td><td>71</td><td>5.21083e-008</td><td>96</td><td>3.11996e-010</td></tr><tr class="text"><td>22</td><td>9.96289e-008</td><td>47</td><td>0.00461024</td><td>72</td><td>4.54413e-005</td><td>97</td><td>1.47642e-007</td></tr><tr class="text"><td>23</td><td>5.97957e-009</td><td>48</td><td>2.03122e-007</td><td>73</td><td>0.00430887</td><td> </td><td> </td></tr><tr class="text"><td>24</td><td>1.98095e-006</td><td>49</td><td>4.63722e-007</td><td>74</td><td>7.08561e-006</td><td> </td><td> </td></tr><tr><td colspan="7" class="grey right">Total log likelihood of joint reconstruction: </td><td class="grey">-1401.13</td></tr>
</table>

|mrof_output=
<align id="mag" folder="mrof"></align>

|sequence_logo=
[[Image:Logo_mag.png|500px|center]]

|hmms=
<pre>
>AP_mag profile HMM generated consensus sequence
lDTGSditlisknvweKlGkpkLeKpvphkikcAngspitvlGrcrVnfelkfGvsytd
pfYVidrgqtnLLGlsWlehspemRda
</pre>

|pairwise_alignment=
<pre>
Domain 1 of 1, from 1 to 86: score 57.8, E = 4.1e-18

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
+DTG+++ ++isk+ +++klg+ ++
AP_mag 1 LDTGSDI-TLISKN--VWEKLGK--------------------PKL- 23

sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
k+ + ++i++a+G+ ++ ++g++r v +++++G
AP_mag 24 EKPVP---HKIKCANGSPIT------VLGRCR------VNFELKFG---- 54

venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
s++ d +++v ++ + +LG+ +L++ + d
AP_mag 55 ---VSYT-D--PFYV--IDR---GQTNLLGL-SWLEHSPEM-RDA 86
</pre>
}}

CAARD:Mag - Revision history

imported>Gydbwiki: CAARD mag