https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&feed=atom&action=historyTask 3: odba human Sequence-based predictions - Revision history2024-03-19T05:28:38ZRevision history for this page on the wikiMediaWiki 1.31.16https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=28726&oldid=prevWagnerr: moved Task 3: obda human Sequence-based predictions to Task 3: odba human Sequence-based predictions2012-12-03T15:12:14Z<p>moved <a href="/wiki/index.php/Task_3:_obda_human_Sequence-based_predictions" class="mw-redirect" title="Task 3: obda human Sequence-based predictions">Task 3: obda human Sequence-based predictions</a> to <a href="/wiki/index.php/Task_3:_odba_human_Sequence-based_predictions" title="Task 3: odba human Sequence-based predictions">Task 3: odba human Sequence-based predictions</a></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<tr class="diff-title" lang="en">
<td colspan="1" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="1" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:12, 3 December 2012</td>
</tr><tr><td colspan="2" class="diff-notice" lang="en"><div class="mw-diff-empty">(No difference)</div>
</td></tr></table>Wagnerrhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=20124&oldid=prevWagnerr: /* GO terms */2012-05-21T22:36:50Z<p><span dir="auto"><span class="autocomment">GO terms</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 22:36, 21 May 2012</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 951:</td>
<td colspan="2" class="diff-lineno">Line 951:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= GO terms =</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= GO terms =</div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The predicted GO Terms from GOPET give a quite good idea of the function of our protein. All predictions with a confidence above 90% are spot on and remakably detailed. However ODBA_human is actually not marked with GO:0004739 (pyruvate dehydrogenase acetyl-transferring activity) or GO:0004738 (pyruvate dehydrogenase activity). It also seems odd, that the hierarchically higher term GO:0004738 is predicted with a lower confidence than the more detailed GO:0004739 term. GOPET predicts for our Protein multiple exclusive categories of dehydrogenases so we would assume that the protein in fact has some kind of dehydrogenase activity. Without further information about the protein it would be hard to decide which of the predicted dehydrogenase categories it actually belongs to, reducing the possible functions to this few select terms is however already a considerable feat.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The predicted GO Terms from GOPET give a quite good idea of the function of our protein. All predictions with a confidence above 90% are spot on and remakably detailed. However ODBA_human is actually not marked with GO:0004739 (pyruvate dehydrogenase acetyl-transferring activity) or GO:0004738 (pyruvate dehydrogenase activity). It also seems odd, that the hierarchically higher term GO:0004738 is predicted with a lower confidence than the more detailed GO:0004739 term. GOPET predicts for our Protein multiple exclusive categories of dehydrogenases so we would assume that the protein in fact has some kind of dehydrogenase activity. Without further information about the protein it would be hard to decide which of the predicted dehydrogenase categories it actually belongs to, reducing the possible functions to this few select terms is however already a considerable feat<ins class="diffchange diffchange-inline">. When searching the sequence of our protein against Pfam we found it belongs to the E1_dh family where the dh stands for dehydrogenase. This further strengthens our assumption that our protein of interest is a dehydrogenase</ins>.</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><table border=1></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><table border=1></div></td>
</tr>
</table>Wagnerrhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=19987&oldid=prevWagnerr: /* GO terms */2012-05-21T19:38:41Z<p><span dir="auto"><span class="autocomment">GO terms</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:38, 21 May 2012</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 951:</td>
<td colspan="2" class="diff-lineno">Line 951:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= GO terms =</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= GO terms =</div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The predicted GO Terms from GOPET give a quite good idea of the function of our protein. All predictions with a confidence above 90% are spot on and remakably detailed. However ODBA_human is actually not marked with GO:0004739(pyruvate dehydrogenase acetyl-transferring activity) or GO:0004738(pyruvate dehydrogenase activity). It also seems odd, that the hierarchically higher term GO:0004738 is predicted with a lower confidence than the more detailed GO:0004739 term. GOPET predicts for our Protein multiple exclusive categories of dehydrogenases so we would assume that the protein in fact has some kind of dehydrogenase activity. Without further information about the protein it would be hard to decide which of the predicted dehydrogenase categories it actually belongs to, reducing the possible functions to this few select terms is however already a considerable feat.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The predicted GO Terms from GOPET give a quite good idea of the function of our protein. All predictions with a confidence above 90% are spot on and remakably detailed. However ODBA_human is actually not marked with GO:0004739<ins class="diffchange diffchange-inline"> </ins>(pyruvate dehydrogenase acetyl-transferring activity) or GO:0004738<ins class="diffchange diffchange-inline"> </ins>(pyruvate dehydrogenase activity). It also seems odd, that the hierarchically higher term GO:0004738 is predicted with a lower confidence than the more detailed GO:0004739 term. GOPET predicts for our Protein multiple exclusive categories of dehydrogenases so we would assume that the protein in fact has some kind of dehydrogenase activity. Without further information about the protein it would be hard to decide which of the predicted dehydrogenase categories it actually belongs to, reducing the possible functions to this few select terms is however already a considerable feat.</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><table border=1></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><table border=1></div></td>
</tr>
<!-- diff cache key wikidb:diff:wikidiff2:1.12:old-19986:rev-19987:1.7.3:0 -->
</table>Wagnerrhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=19986&oldid=prevWagnerr: /* GO terms */2012-05-21T19:38:08Z<p><span dir="auto"><span class="autocomment">GO terms</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:38, 21 May 2012</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 951:</td>
<td colspan="2" class="diff-lineno">Line 951:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= GO terms =</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= GO terms =</div></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The predicted GO Terms from GOPET give a quite good idea of the function of our protein. All predictions with a confidence above 90% are spot on and remakably detailed. However ODBA_human is actually not marked with GO:0004739(pyruvate dehydrogenase acetyl-transferring activity) or GO:0004738(pyruvate dehydrogenase activity). It also seems odd, that the hierarchically higher term GO:0004738 is predicted with a lower confidence than the more detailed GO:0004739 term. GOPET predicts for our Protein multiple exclusive categories of dehydrogenases so we would assume that the protein in fact has some kind of dehydrogenase activity. Without further information about the protein it would be hard to decide which of the predicted dehydrogenase categories it actually belongs to, reducing the possible functions to this few select terms is however already a considerable feat.</div></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><table border=1></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><table border=1></div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><tr><td colspan=4 align=center><b>GOPET</b></td></tr></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><tr><td colspan=4 align=center><b>GOPET</b></td></tr></div></td>
</tr>
<tr>
<td colspan="2" class="diff-lineno">Line 968:</td>
<td colspan="2" class="diff-lineno">Line 970:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><tr><td>GO:0046872</td><td>F</td><td>62%</td><td>metal ion binding</td></tr></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><tr><td>GO:0046872</td><td>F</td><td>62%</td><td>metal ion binding</td></tr></div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></table></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></table></div></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Unfortunately applying ProtFun to determine the protein function did not really help very much. There is only one statement that has a confidence value above 33%, which is, that the Protein is an enzyme (76.9%).</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> ############## ProtFun 2.2 predictions ##############</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> ############## ProtFun 2.2 predictions ##############</div></td>
</tr>
<tr>
<td colspan="2" class="diff-lineno">Line 1,016:</td>
<td colspan="2" class="diff-lineno">Line 1,021:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> //</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> //</div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"></td>
<td colspan="2" class="diff-empty"> </td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Unfortunately applying ProtFun to determine the protein function did not really help very much. There is only one statement that has a confidence value above 33%, which is, that the Protein is an enzyme (76.9%).</div></td>
<td colspan="2" class="diff-empty"> </td>
</tr>
<!-- diff cache key wikidb:diff:wikidiff2:1.12:old-19961:rev-19986:1.7.3:0 -->
</table>Wagnerrhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=19961&oldid=prevWagnerr: /* Signal peptides */2012-05-21T18:57:26Z<p><span dir="auto"><span class="autocomment">Signal peptides</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:57, 21 May 2012</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 948:</td>
<td colspan="2" class="diff-lineno">Line 948:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The default cutoff for SignalPv3 to consider a Protein to be a signal Protein is 0.48 for the Mean-S-score. So according to the old version of SignalP our protein would be classified as a signal peptide. When using the D-score (a weighted average of the S-mean and the Y-max scores), which is supposed to show the best discrimination, ODBA_Human would fall just below the cutoff (0.425/0.430) and would no longer be classified as signal peptide. In all other cases there was no disagreement between Mean-S and D score. The HMM prediction produced quite high confidence values for all four proteins, even when the Mean-S and D values from the neural network prediction indicated otherwise. We were unable to obtain any HMM predictions for the web version of SignalPv4. We are not sure if this is just a limitation of the web platform, or if this prediction method was depreciated.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The default cutoff for SignalPv3 to consider a Protein to be a signal Protein is 0.48 for the Mean-S-score. So according to the old version of SignalP our protein would be classified as a signal peptide. When using the D-score (a weighted average of the S-mean and the Y-max scores), which is supposed to show the best discrimination, ODBA_Human would fall just below the cutoff (0.425/0.430) and would no longer be classified as signal peptide. In all other cases there was no disagreement between Mean-S and D score. The HMM prediction produced quite high confidence values for all four proteins, even when the Mean-S and D values from the neural network prediction indicated otherwise. We were unable to obtain any HMM predictions for the web version of SignalPv4. We are not sure if this is just a limitation of the web platform, or if this prediction method was depreciated.</div></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Checking the predictions with SignalPeptide.de proved difficult, as for P02768 neither searching for UniprotID (ALBU_HUMAN) nor Accesion number (P02768) or sequence retrieved any results, only searching for the trivial name Serum albumin scored any results.We had the same problem with P11279. For P47863 and ODBA_Human we found no entries in SignalPeptide.de <del class="diffchange diffchange-inline">or</del> in UniProt <del class="diffchange diffchange-inline">that</del> <del class="diffchange diffchange-inline">indicate</del> <del class="diffchange diffchange-inline">towards</del> <del class="diffchange diffchange-inline">these</del> <del class="diffchange diffchange-inline">Proteins</del> <del class="diffchange diffchange-inline">being</del> signal peptides.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Checking the predictions with SignalPeptide.de proved difficult, as for P02768 neither searching for UniprotID (ALBU_HUMAN) nor Accesion number (P02768) or sequence retrieved any results, only searching for the trivial name Serum albumin scored any results.<ins class="diffchange diffchange-inline"> </ins>We had the same problem with P11279. For P47863 and ODBA_Human we found no entries in SignalPeptide.de<ins class="diffchange diffchange-inline">. UniProt however marks the OBDA_human sequence from position 1 to 45 as a transit peptide domain, and notes it's cellular location as mitochondrial. While this directly contradicts the SignalP prediction, it seems likely for a protein that metabolizes amino acids to be</ins> <ins class="diffchange diffchange-inline">located in the mitochondria. For P47863 a lookup</ins> in UniProt<ins class="diffchange diffchange-inline">,</ins> <ins class="diffchange diffchange-inline">as</ins> <ins class="diffchange diffchange-inline">well</ins> <ins class="diffchange diffchange-inline">as</ins> <ins class="diffchange diffchange-inline">the</ins> <ins class="diffchange diffchange-inline">prediction</ins> <ins class="diffchange diffchange-inline">from PolyPhobius identified the protein as a membrane protein. These seem to be quite similar to</ins> signal peptides<ins class="diffchange diffchange-inline">, which might explain the predicted likelyhood of 72.3% with the HMM aproach in PolyPhobiusv3</ins>.</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= GO terms =</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= GO terms =</div></td>
</tr>
<!-- diff cache key wikidb:diff:wikidiff2:1.12:old-19953:rev-19961:1.7.3:0 -->
</table>Wagnerrhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=19953&oldid=prevKiening: /* Comparison */2012-05-21T18:47:16Z<p><span dir="auto"><span class="autocomment">Comparison</span></span></p>
<a href="https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=19953&oldid=19947">Show changes</a>Kieninghttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=19947&oldid=prevKiening: /* Comparison */2012-05-21T18:32:48Z<p><span dir="auto"><span class="autocomment">Comparison</span></span></p>
<a href="https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=19947&oldid=19945">Show changes</a>Kieninghttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=19945&oldid=prevKiening: /* Comparison */2012-05-21T18:31:35Z<p><span dir="auto"><span class="autocomment">Comparison</span></span></p>
<a href="https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=19945&oldid=19944">Show changes</a>Kieninghttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=19944&oldid=prevWagnerr: /* GO terms */2012-05-21T18:30:17Z<p><span dir="auto"><span class="autocomment">GO terms</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:30, 21 May 2012</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 1,016:</td>
<td colspan="2" class="diff-lineno">Line 1,016:</td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> //</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> //</div></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Unfortunately applying ProtFun to determine the protein function did not really help very much. There is only one statement that has a confidence value above 33%, which is, that the Protein is an enzyme (76.9%).</div></td>
</tr>
</table>Wagnerrhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=19942&oldid=prevKiening: /* Comparison */2012-05-21T18:27:32Z<p><span dir="auto"><span class="autocomment">Comparison</span></span></p>
<a href="https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Task_3:_odba_human_Sequence-based_predictions&diff=19942&oldid=19941">Show changes</a>Kiening