CAARD:Alpharetroviridae - Revision history

imported>Gydbwiki: New page: {{CAARD |pin_output= (RSV:0.363657,LPDV:0.717462,EAV-HP:0.238126); |fin_output=

Name Father Distance to father So...
2009-05-08T12:04:00Z

New page: {{CAARD |pin_output= (RSV:0.363657,LPDV:0.717462,EAV-HP:0.238126); |fin_output= <table class="tabdata"> <tr class="grey"> <td>Name</td> <td>Father</td> <td>Distance to father</td> <td>So...

New page
{{CAARD
|pin_output=
(RSV:0.363657,LPDV:0.717462,EAV-HP:0.238126);

|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>RSV</td><td>N1</td><td>0.363657</td><td>-</td></tr><tr><td>LPDV</td><td>N1</td><td>0.717462</td><td>-</td></tr><tr><td>EAV-HP</td><td>N1</td><td>0.238126</td><td>-</td></tr><tr><td>N1</td><td>root!</td><td>-</td><td>RSV LPDV EAV-HP</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>0.00117484</td><td>22</td><td>0.0358256</td><td>44</td><td>0.000505241</td><td>66</td><td>0.0164059</td></tr><tr class="text"><td>1</td><td>0.01426</td><td>23</td><td>0.00166365</td><td>45</td><td>0.000823669</td><td>67</td><td>2.37143e-006</td></tr><tr class="text"><td>2</td><td>0.00273671</td><td>24</td><td>0.000327972</td><td>46</td><td>0.00278983</td><td>68</td><td>0.00531678</td></tr><tr class="text"><td>3</td><td>0.0318332</td><td>25</td><td>4.13047e-006</td><td>47</td><td>0.000254718</td><td>69</td><td>1.36305e-005</td></tr><tr class="text"><td>4</td><td>0.0164059</td><td>26</td><td>0.000117663</td><td>48</td><td>0.000256299</td><td>70</td><td>0.000134614</td></tr><tr class="text"><td>5</td><td>0.01426</td><td>27</td><td>0.028095</td><td>49</td><td>0.0116073</td><td>71</td><td>0.000137404</td></tr><tr class="text"><td>6</td><td>0.00277929</td><td>28</td><td>0.0052105</td><td>50</td><td>0.000433897</td><td>72</td><td>0.000673734</td></tr><tr class="text"><td>7</td><td>0.0110915</td><td>29</td><td>5.31937e-007</td><td>51</td><td>0.0142713</td><td>73</td><td>0.0396324</td></tr><tr class="text"><td>8</td><td>0.00277929</td><td>30</td><td>0.0318332</td><td>52</td><td>0.00491497</td><td>74</td><td>0.0318332</td></tr><tr class="text"><td>9</td><td>0.00176035</td><td>31</td><td>0.00277929</td><td>53</td><td>0.049833</td><td>75</td><td>0.0142713</td></tr><tr class="text"><td>10</td><td>0.00014966</td><td>32</td><td>0.0318332</td><td>54</td><td>0.0296955</td><td>76</td><td>0.00491497</td></tr><tr class="text"><td>11</td><td>0.0193496</td><td>33</td><td>0.0318332</td><td>55</td><td>0.000472403</td><td>77</td><td>3.15422e-006</td></tr><tr class="text"><td>12</td><td>1.12642e-005</td><td>34</td><td>4.8452e-005</td><td>56</td><td>0.0193496</td><td>78</td><td>0.0396324</td></tr><tr class="text"><td>13</td><td>9.37352e-005</td><td>35</td><td>0.0005937</td><td>57</td><td>0.00414389</td><td>79</td><td>0.00107153</td></tr><tr class="text"><td>14</td><td>0.0094486</td><td>36</td><td>0.000377385</td><td>58</td><td>0.000356308</td><td>80</td><td>0.0107323</td></tr><tr class="text"><td>15</td><td>0.0199208</td><td>37</td><td>1.57754e-005</td><td>59</td><td>2.26491e-005</td><td>81</td><td>1.30637e-005</td></tr><tr class="text"><td>16</td><td>5.93246e-005</td><td>38</td><td>0.000935726</td><td>60</td><td>0.000713136</td><td>82</td><td>0.000166897</td></tr><tr class="text"><td>17</td><td>5.23323e-005</td><td>39</td><td>0.00202355</td><td>61</td><td>0.00371725</td><td>83</td><td>0.000360101</td></tr><tr class="text"><td>18</td><td>0.0094486</td><td>40</td><td>0.0115495</td><td>62</td><td>1.21437e-005</td><td>84</td><td>6.35115e-005</td></tr><tr class="text"><td>19</td><td>0.0199208</td><td>41</td><td>7.47892e-006</td><td>63</td><td>0.0199208</td><td>85</td><td>0.0283661</td></tr><tr class="text"><td>20</td><td>0.00123063</td><td>42</td><td>1.1048e-005</td><td>64</td><td>5.57873e-006</td><td>86</td><td>0.00371725</td></tr><tr class="text"><td>21</td><td>0.0015665</td><td>43</td><td>6.40288e-006</td><td>65</td><td>0.00531678</td><td> </td><td> </td></tr><tr><td colspan="7" class="grey right">Total log likelihood of joint reconstruction: </td><td class="grey">-597.807</td></tr>
</table>

|jrof_output=
<align id="alpharetroviridae" 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>0.00146915</td><td>22</td><td>0.0365767</td><td>44</td><td>0.000964977</td><td>66</td><td>0.0165011</td></tr><tr class="text"><td>1</td><td>0.0143427</td><td>23</td><td>0.00173393</td><td>45</td><td>0.000887219</td><td>67</td><td>9.4539e-006</td></tr><tr class="text"><td>2</td><td>0.00289206</td><td>24</td><td>0.000692302</td><td>46</td><td>0.00491213</td><td>68</td><td>0.0057405</td></tr><tr class="text"><td>3</td><td>0.0318478</td><td>25</td><td>9.59089e-006</td><td>47</td><td>0.000275119</td><td>69</td><td>3.00893e-005</td></tr><tr class="text"><td>4</td><td>0.0165011</td><td>26</td><td>0.000159815</td><td>48</td><td>0.000269403</td><td>70</td><td>0.000136978</td></tr><tr class="text"><td>5</td><td>0.0143427</td><td>27</td><td>0.040752</td><td>49</td><td>0.0117445</td><td>71</td><td>0.00032452</td></tr><tr class="text"><td>6</td><td>0.00358495</td><td>28</td><td>0.00556649</td><td>50</td><td>0.000447465</td><td>72</td><td>0.000898795</td></tr><tr class="text"><td>7</td><td>0.0111468</td><td>29</td><td>1.67886e-006</td><td>51</td><td>0.0143203</td><td>73</td><td>0.039697</td></tr><tr class="text"><td>8</td><td>0.00358495</td><td>30</td><td>0.0318478</td><td>52</td><td>0.00517398</td><td>74</td><td>0.0318478</td></tr><tr class="text"><td>9</td><td>0.00276598</td><td>31</td><td>0.00358495</td><td>53</td><td>0.0501146</td><td>75</td><td>0.0143203</td></tr><tr class="text"><td>10</td><td>0.00025867</td><td>32</td><td>0.0318478</td><td>54</td><td>0.0306957</td><td>76</td><td>0.00517398</td></tr><tr class="text"><td>11</td><td>0.019458</td><td>33</td><td>0.0318478</td><td>55</td><td>0.000481192</td><td>77</td><td>6.45175e-006</td></tr><tr class="text"><td>12</td><td>2.20432e-005</td><td>34</td><td>7.13023e-005</td><td>56</td><td>0.019458</td><td>78</td><td>0.039697</td></tr><tr class="text"><td>13</td><td>0.000195066</td><td>35</td><td>0.000658171</td><td>57</td><td>0.00687743</td><td>79</td><td>0.001706</td></tr><tr class="text"><td>14</td><td>0.00944862</td><td>36</td><td>0.000385085</td><td>58</td><td>0.000361199</td><td>80</td><td>0.0107464</td></tr><tr class="text"><td>15</td><td>0.0199288</td><td>37</td><td>3.49291e-005</td><td>59</td><td>8.37657e-005</td><td>81</td><td>2.53568e-005</td></tr><tr class="text"><td>16</td><td>8.00944e-005</td><td>38</td><td>0.000953747</td><td>60</td><td>0.000722594</td><td>82</td><td>0.000852876</td></tr><tr class="text"><td>17</td><td>8.66336e-005</td><td>39</td><td>0.00237517</td><td>61</td><td>0.00381902</td><td>83</td><td>0.000364597</td></tr><tr class="text"><td>18</td><td>0.00944862</td><td>40</td><td>0.0116398</td><td>62</td><td>3.05705e-005</td><td>84</td><td>0.000146116</td></tr><tr class="text"><td>19</td><td>0.0199288</td><td>41</td><td>2.20451e-005</td><td>63</td><td>0.0199288</td><td>85</td><td>0.0288485</td></tr><tr class="text"><td>20</td><td>0.00139821</td><td>42</td><td>1.58606e-005</td><td>64</td><td>1.05485e-005</td><td>86</td><td>0.00381902</td></tr><tr class="text"><td>21</td><td>0.00272833</td><td>43</td><td>1.10597e-005</td><td>65</td><td>0.0057405</td><td> </td><td> </td></tr><tr><td colspan="7" class="grey right">Total log likelihood of joint reconstruction: </td><td class="grey">-572.891</td></tr>
</table>

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

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

|hmms=
<pre>
>AP_alpharetroviridae profile HMM generated consensus sequence [hmmemit]
LDsGADvTvisEtdWPssWPaiEasqsqieGvGGatpsrrSenlvqagvInRdGSlEkp
illtPlvAavrgtiLGRdaLrQihgvRl
</pre>

|pairwise_alignment=
<pre>
domain 1 of 1, from 1 to 87: score 40.7, E = 5.7e-13

DTG_ILG template ->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
+D+GA+v +vis + + ++ s+P
AP_alphare 1 LDSGADV-TVIS----ETD-WPS--------------------SWPA 21

sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
++s q++i g+gG ++++ +++ ++q ++ ++G++
AP_alphare 22 IEAS---QSQIEGVGGATPSR--RSENLVQ--------AGVINRDGSL-- 56

venrsl.psdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-
+++ + + +lv+ + ILGr d Lrq ++ ++l
AP_alphare 57 ---EKPiLLT--PLVA-AVR-----G-TILGR-DALRQIHG--VRL 87
</pre>
}}