CAARD:Deltaretroviridae - Revision history

imported>Gydbwiki: New page: {{CAARD |pin_output= (STcLV2PP:0.173401,HTLV-2:0.201136,(HTLV-1:0.276098,BLV:0.665907)N2:0.028256); |fin_output=

Name Father...
2009-05-08T13:19:08Z

New page: {{CAARD |pin_output= (STcLV2PP:0.173401,HTLV-2:0.201136,(HTLV-1:0.276098,BLV:0.665907)N2:0.028256); |fin_output= <table class="tabdata"> <tr class="grey"> <td>Name</td> <td>Father...

New page
{{CAARD
|pin_output=
(STcLV2PP:0.173401,HTLV-2:0.201136,(HTLV-1:0.276098,BLV:0.665907)N2:0.028256);

|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>STcLV2PP</td><td>N1</td><td>0.173401</td><td>-</td></tr><tr><td>HTLV-2</td><td>N1</td><td>0.201136</td><td>-</td></tr><tr><td>HTLV-1</td><td>N2</td><td>0.276098</td><td>-</td></tr><tr><td>BLV</td><td>N2</td><td>0.665907</td><td>-</td></tr><tr><td>N1</td><td>root!</td><td>-</td><td>STcLV2PP HTLV-2 N2</td></tr><tr><td>N2</td><td>N1</td><td>0.028256</td><td>HTLV-1 BLV</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>0.00335036</td><td>25</td><td>0.0177157</td><td>50</td><td>0.0592915</td><td>75</td><td>0.000562148</td></tr><tr class="text"><td>1</td><td>0.0136762</td><td>26</td><td>1.11403e-005</td><td>51</td><td>0.0344702</td><td>76</td><td>0.00937192</td></tr><tr class="text"><td>2</td><td>0.0105441</td><td>27</td><td>0.0037952</td><td>52</td><td>0.0592915</td><td>77</td><td>2.46199e-005</td></tr><tr class="text"><td>3</td><td>0.0311957</td><td>28</td><td>0.000275664</td><td>53</td><td>1.32125e-008</td><td>78</td><td>0.01097</td></tr><tr class="text"><td>4</td><td>0.0156187</td><td>29</td><td>0.0790284</td><td>54</td><td>1.90757e-005</td><td>79</td><td>0.00222891</td></tr><tr class="text"><td>5</td><td>0.00437991</td><td>30</td><td>0.00145989</td><td>55</td><td>1.879e-008</td><td>80</td><td>0.0311957</td></tr><tr class="text"><td>6</td><td>7.34474e-006</td><td>31</td><td>0.038708</td><td>56</td><td>0.000320615</td><td>81</td><td>0.0137505</td></tr><tr class="text"><td>7</td><td>0.0105441</td><td>32</td><td>0.0311957</td><td>57</td><td>0.0194846</td><td>82</td><td>0.0136762</td></tr><tr class="text"><td>8</td><td>0.0140964</td><td>33</td><td>0.0156187</td><td>58</td><td>0.0173713</td><td>83</td><td>1.26944e-005</td></tr><tr class="text"><td>9</td><td>0.000966719</td><td>34</td><td>0.000838808</td><td>59</td><td>0.00020567</td><td>84</td><td>0.038708</td></tr><tr class="text"><td>10</td><td>0.0194846</td><td>35</td><td>0.0311957</td><td>60</td><td>1.13199e-005</td><td>85</td><td>0.000445848</td></tr><tr class="text"><td>11</td><td>2.70168e-005</td><td>36</td><td>0.000199454</td><td>61</td><td>5.07906e-006</td><td>86</td><td>4.18938e-005</td></tr><tr class="text"><td>12</td><td>3.60608e-005</td><td>37</td><td>0.00254954</td><td>62</td><td>0.0194846</td><td>87</td><td>0.000204005</td></tr><tr class="text"><td>13</td><td>0.0588794</td><td>38</td><td>2.78071e-007</td><td>63</td><td>3.03271e-005</td><td>88</td><td>0.0103743</td></tr><tr class="text"><td>14</td><td>2.22703e-008</td><td>39</td><td>1.14145e-006</td><td>64</td><td>4.9756e-005</td><td>89</td><td>6.52163e-005</td></tr><tr class="text"><td>15</td><td>0.00182765</td><td>40</td><td>5.07464e-005</td><td>65</td><td>0.038708</td><td>90</td><td>2.40935e-005</td></tr><tr class="text"><td>16</td><td>6.51069e-007</td><td>41</td><td>0.00201139</td><td>66</td><td>6.00089e-005</td><td>91</td><td>0.00328935</td></tr><tr class="text"><td>17</td><td>0.0306601</td><td>42</td><td>0.00134702</td><td>67</td><td>0.0263603</td><td>92</td><td>0.000466942</td></tr><tr class="text"><td>18</td><td>0.000767098</td><td>43</td><td>0.000236969</td><td>68</td><td>0.0135013</td><td>93</td><td>0.00328935</td></tr><tr class="text"><td>19</td><td>0.000128123</td><td>44</td><td>0.000231898</td><td>69</td><td>0.0588794</td><td>94</td><td>0.0194846</td></tr><tr class="text"><td>20</td><td>3.79375e-006</td><td>45</td><td>0.000133794</td><td>70</td><td>0.000537525</td><td>95</td><td>0.00146246</td></tr><tr class="text"><td>21</td><td>0.000641099</td><td>46</td><td>1.7857e-006</td><td>71</td><td>0.0136762</td><td>96</td><td>8.80624e-005</td></tr><tr class="text"><td>22</td><td>1.16823e-005</td><td>47</td><td>0.0194846</td><td>72</td><td>0.0105441</td><td> </td><td> </td></tr><tr class="text"><td>23</td><td>1.7178e-006</td><td>48</td><td>0.00131973</td><td>73</td><td>5.26516e-008</td><td> </td><td> </td></tr><tr class="text"><td>24</td><td>0.0790284</td><td>49</td><td>0.0246673</td><td>74</td><td>9.94145e-005</td><td> </td><td> </td></tr><tr><td colspan="7" class="grey right">Total log likelihood of joint reconstruction: </td><td class="grey">-710.58</td></tr>
</table>

|jrof_output=
<align id="deltaretroviridae" 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>0.00336122</td><td>25</td><td>0.022944</td><td>50</td><td>0.091904</td><td>75</td><td>0.000569197</td></tr><tr class="text"><td>1</td><td>0.013687</td><td>26</td><td>1.39118e-005</td><td>51</td><td>0.076748</td><td>76</td><td>0.00937192</td></tr><tr class="text"><td>2</td><td>0.0105502</td><td>27</td><td>0.00391318</td><td>52</td><td>0.091904</td><td>77</td><td>2.71428e-005</td></tr><tr class="text"><td>3</td><td>0.0311973</td><td>28</td><td>0.000318086</td><td>53</td><td>2.23671e-008</td><td>78</td><td>0.0109891</td></tr><tr class="text"><td>4</td><td>0.0156298</td><td>29</td><td>0.091904</td><td>54</td><td>2.41384e-005</td><td>79</td><td>0.00224288</td></tr><tr class="text"><td>5</td><td>0.00441295</td><td>30</td><td>0.00157341</td><td>55</td><td>3.73566e-008</td><td>80</td><td>0.0311973</td></tr><tr class="text"><td>6</td><td>9.14812e-006</td><td>31</td><td>0.0387159</td><td>56</td><td>0.000321391</td><td>81</td><td>0.0137565</td></tr><tr class="text"><td>7</td><td>0.0105502</td><td>32</td><td>0.0311973</td><td>57</td><td>0.0194854</td><td>82</td><td>0.013687</td></tr><tr class="text"><td>8</td><td>0.0141274</td><td>33</td><td>0.0156298</td><td>58</td><td>0.0173727</td><td>83</td><td>1.77888e-005</td></tr><tr class="text"><td>9</td><td>0.000979429</td><td>34</td><td>0.000843902</td><td>59</td><td>0.000206124</td><td>84</td><td>0.0387159</td></tr><tr class="text"><td>10</td><td>0.0194854</td><td>35</td><td>0.0311973</td><td>60</td><td>1.99805e-005</td><td>85</td><td>0.000446589</td></tr><tr class="text"><td>11</td><td>2.71847e-005</td><td>36</td><td>0.000199738</td><td>61</td><td>1.15331e-005</td><td>86</td><td>4.66366e-005</td></tr><tr class="text"><td>12</td><td>4.38057e-005</td><td>37</td><td>0.002563</td><td>62</td><td>0.0194854</td><td>87</td><td>0.000204057</td></tr><tr class="text"><td>13</td><td>0.0589482</td><td>38</td><td>9.33953e-007</td><td>63</td><td>3.70333e-005</td><td>88</td><td>0.0103758</td></tr><tr class="text"><td>14</td><td>4.10492e-008</td><td>39</td><td>3.80209e-006</td><td>64</td><td>5.97147e-005</td><td>89</td><td>7.09177e-005</td></tr><tr class="text"><td>15</td><td>0.0032753</td><td>40</td><td>5.84148e-005</td><td>65</td><td>0.0387159</td><td>90</td><td>2.57568e-005</td></tr><tr class="text"><td>16</td><td>1.1079e-006</td><td>41</td><td>0.00201793</td><td>66</td><td>0.000118587</td><td>91</td><td>0.00330082</td></tr><tr class="text"><td>17</td><td>0.066005</td><td>42</td><td>0.0013504</td><td>67</td><td>0.0264607</td><td>92</td><td>0.000467389</td></tr><tr class="text"><td>18</td><td>0.00123554</td><td>43</td><td>0.000237292</td><td>68</td><td>0.0135029</td><td>93</td><td>0.00330082</td></tr><tr class="text"><td>19</td><td>0.000207749</td><td>44</td><td>0.000235106</td><td>69</td><td>0.0589482</td><td>94</td><td>0.0194854</td></tr><tr class="text"><td>20</td><td>8.96983e-006</td><td>45</td><td>0.000134645</td><td>70</td><td>0.000548147</td><td>95</td><td>0.00152761</td></tr><tr class="text"><td>21</td><td>0.000646159</td><td>46</td><td>2.35203e-006</td><td>71</td><td>0.013687</td><td>96</td><td>9.68826e-005</td></tr><tr class="text"><td>22</td><td>1.44494e-005</td><td>47</td><td>0.0194854</td><td>72</td><td>0.0105502</td><td> </td><td> </td></tr><tr class="text"><td>23</td><td>1.83724e-006</td><td>48</td><td>0.00134214</td><td>73</td><td>1.41382e-007</td><td> </td><td> </td></tr><tr class="text"><td>24</td><td>0.091904</td><td>49</td><td>0.058565</td><td>74</td><td>0.000102332</td><td> </td><td> </td></tr><tr><td colspan="7" class="grey right">Total log likelihood of joint reconstruction: </td><td class="grey">-693.255</td></tr>
</table>

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

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

|hmms=
<pre>
>AP_deltaretroviridae profile HMM generated consensus sequence [hmmemit]
lDTGAdlTVLPqaLvpsvedvPvkdttVLGAGGqtrnqFkllqsPLtlalkielPFrtt
PviLsSCLVDTknkWaIiGRDvLqqcQgvlylPed
</pre>

|pairwise_alignment=
<pre>
domain 1 of 1, from 1 to 90: score 42.3, E = 1.8e-13

DTG_ILG template ->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
+DTGA++ +v+++ l+ + P
AP_deltare 1 LDTGADL-TVLPQA--LVPSVE---------------------DVPV 23

sktsttaqdtirgagGqs..kiyvSklktsgqirknllslvtikitkGnv
++t+ + gagGq++++ ++ q++ l+++++i++
AP_deltare 24 KDTT------VLGAGGQTrnQF------KLLQSP--LTLALKIEL--P-- 55

Tevenrslpsdgvflvv.tdpedqks.rydvILGrldfLrqlnsvhidl<-
+ ++ +++++ +++d +++++ +I+Gr d+L+q+++ + +
AP_deltare 56 -------FRTT--PVILsSCLVD-TKnKW-AIIGR-DVLQQCQG--VLY 90
</pre>
}}