https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Prediction_of_transmembrane_alpha-helices_and_signal_peptides_HEXA_HUMAN&feed=atom&action=history
Prediction of transmembrane alpha-helices and signal peptides HEXA HUMAN - Revision history
2024-03-29T07:37:22Z
Revision history for this page on the wiki
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Link at 21:03, 30 August 2011
2011-08-30T21:03:39Z
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<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 21:03, 30 August 2011</td>
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<td colspan="2" class="diff-lineno">Line 3:</td>
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<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>First of all, we analysed the protein with TMHMM.</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>First of all, we analysed the protein with TMHMM.</div></td>
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<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>
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<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>
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<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>[[Image:hexa_human_tmhmm.png|thumb|Prediction of TMHMM for the transmembrane helices of HEXA_HUMAN]]</div></td>
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<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>[[Image:hexa_human_tmhmm.png|thumb|<ins class="diffchange diffchange-inline">Figure 1: </ins>Prediction of TMHMM for the transmembrane helices of HEXA_HUMAN]]</div></td>
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<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>
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<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>
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<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>TMHMM predicts no transmembrane helix at all. The whole protein is located at the extracellular space. To evaluate this result, we compared the data from UniProt with our prediction.</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>TMHMM predicts no transmembrane helix at all<ins class="diffchange diffchange-inline">, which can be seen on Figure 1</ins>. The whole protein is located at the extracellular space. To evaluate this result, we compared the data from<ins class="diffchange diffchange-inline"> [[http://www.uniprot.org/</ins> UniProt<ins class="diffchange diffchange-inline">]]</ins> with our prediction.</div></td>
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<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>
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<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>[[Image:hexa_human_tmhmm_vs_real.png|center|thumb|Comparison between real <del class="diffchange diffchange-inline">occuring</del> transmembrane helices and the TMHMM result.]]</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>[[Image:hexa_human_tmhmm_vs_real.png|center|thumb|<ins class="diffchange diffchange-inline">Figure 2: </ins>Comparison between real <ins class="diffchange diffchange-inline">occurring</ins> transmembrane helices and the TMHMM result.]]</div></td>
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<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>
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<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>As you can see above, the TMHMM prediction result is <del class="diffchange diffchange-inline">completly</del> right, expect of the signal peptide, which can't be predicted by TMHMM.</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>As you can see above<ins class="diffchange diffchange-inline"> (Figure 2)</ins>, the TMHMM prediction result is <ins class="diffchange diffchange-inline">completely</ins> right, expect of the signal peptide, which can't be predicted by TMHMM.</div></td>
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<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><br><br></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><br><br></div></td>
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<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>Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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>Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></div></td>
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<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>=== Phobius and PolyPhobius ===</div></td>
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<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>=== Phobius and PolyPhobius ===</div></td>
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<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>
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<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>Next, we used Phobius and also PolyPhobius to predict the transmembrane helices and also the <del class="diffchange diffchange-inline">signale</del> peptide.</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>Next, we used Phobius and also PolyPhobius to predict the transmembrane helices and also the <ins class="diffchange diffchange-inline">signal</ins> peptide.</div></td>
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<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>
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<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>[[Image:phobius.png|thumb|Prediction of Phobius for the transmembrane helices and signal peptides of HEXA_HUMAN]]</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>[[Image:phobius.png|thumb|<ins class="diffchange diffchange-inline">Figure 3: </ins>Prediction of Phobius for the transmembrane helices and signal peptides of HEXA_HUMAN]]</div></td>
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<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>[[Image:polyphobius.png|thumb|Prediction of PolyPhobius for the transmembrane helices and signal peptides of HEXA_HUMAN]]</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>[[Image:polyphobius.png|thumb|<ins class="diffchange diffchange-inline">Figure 4: </ins>Prediction of PolyPhobius for the transmembrane helices and signal peptides of HEXA_HUMAN]]</div></td>
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<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>
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<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>
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<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>{| border="1" style="text-align:center; border-spacing:0;"</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>{| border="1" style="text-align:center; border-spacing:0;"</div></td>
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<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>
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<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>
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<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>Both methods <del class="diffchange diffchange-inline">don't</del> predict a transmembrane helix, which is correct, because HEXA_HUMAN is located at the lysosmal space.</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>Both methods <ins class="diffchange diffchange-inline">do not</ins> predict a transmembrane helix<ins class="diffchange diffchange-inline"> (compare Figure 3 and Figure 4)</ins>, which is correct, because HEXA_HUMAN is located at the lysosmal space.</div></td>
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<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>We compared the results of Phobius and PolyPhobius with the real protein.</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>We compared the results of Phobius and PolyPhobius with the real protein.</div></td>
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<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><br><br></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><br><br></div></td>
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<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>Comparison with the real structure of the protein:</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>Comparison with the real structure of the protein:</div></td>
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<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>
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<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>| [[Image:hexa_phobius_vs_real.png|thumb|Comparison between the prediction of Phobius and the real protein]]</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>| [[Image:hexa_phobius_vs_real.png|thumb|<ins class="diffchange diffchange-inline">Figure 5: </ins>Comparison between the prediction of Phobius and the real protein]]</div></td>
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<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>| [[Image:hexa_poly_vs_real.png|thumb|Comparison between the prediction of PolyPhobius and the real protein]]</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>| [[Image:hexa_poly_vs_real.png|thumb|<ins class="diffchange diffchange-inline">Figure 6: </ins>Comparison between the prediction of PolyPhobius and the real protein]]</div></td>
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<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;"></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="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 prediction of Phobius is a little bit better than the PolyPhobius prediction, because Phobius predicts the beginning and the end of the signal peptide totally correct, whereas PolyPhobius cuts two residues of the signal peptide.</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 prediction of Phobius<ins class="diffchange diffchange-inline"> (Figure 5)</ins> is a little bit better than the PolyPhobius prediction<ins class="diffchange diffchange-inline"> (Figure 6)</ins>, because Phobius predicts the beginning and the end of the signal peptide totally correct, whereas PolyPhobius cuts two residues of the signal peptide.</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><br><br></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><br><br></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>Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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>Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></div></td>
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<tr>
<td colspan="2" class="diff-lineno">Line 100:</td>
<td colspan="2" class="diff-lineno">Line 100:</td>
</tr>
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<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>As next tools we used OCTOPUS and SPOCTOPUS to predict the transmembrane helices and the signal peptide again.</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>As next tools we used OCTOPUS and SPOCTOPUS to predict the transmembrane helices and the signal peptide again.</div></td>
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<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><br><br></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><br><br></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>[[Image:hexa_human_octopus.png|thumb|Prediction of OCTOPUS for the transmembrane helices of HEXA_HUMAN]]</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>[[Image:hexa_human_octopus.png|thumb|<ins class="diffchange diffchange-inline">Figure 7: </ins>Prediction of OCTOPUS for the transmembrane helices of HEXA_HUMAN]]</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>[[Image:hexa_human_spoctopus.png|thumb|Prediction of SPOCTOPUS for the transmembrane helices of HEXA_HUMAN]]</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>[[Image:hexa_human_spoctopus.png|thumb|<ins class="diffchange diffchange-inline">Figure 8: </ins>Prediction of SPOCTOPUS for the transmembrane helices of HEXA_HUMAN]]</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>{| border="1" style="text-align:center; border-spacing:0;"</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>{| border="1" style="text-align:center; border-spacing:0;"</div></td>
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<tr>
<td colspan="2" class="diff-lineno">Line 138:</td>
<td colspan="2" class="diff-lineno">Line 138:</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 results of these two predictions differ. </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 results of these two predictions differ. </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>OCTOPUS predicts a transmembrane helix, whereas SPOCTOPUS predicts at the same location a signal peptide.</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>OCTOPUS predicts a transmembrane helix<ins class="diffchange diffchange-inline"> (Figure 7)</ins>, whereas SPOCTOPUS predicts at the same location a signal peptide<ins class="diffchange diffchange-inline"> (Figure 8)</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;"><div><br></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><br></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>To check which method predicted right, we compared the protein and the prediction.</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>To check which method predicted right, we compared the protein and the prediction.</div></td>
</tr>
<tr>
<td colspan="2" class="diff-lineno">Line 144:</td>
<td colspan="2" class="diff-lineno">Line 144:</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>Comparison with the real structure of the protein:</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>Comparison with the real structure of the protein:</div></td>
</tr>
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<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;"><div>| [[Image:hexa_human_octopus_vs_real.png|thumb|Comparison between the prediction of OCTOPUS and the real protein]]</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>| [[Image:hexa_human_octopus_vs_real.png|thumb|<ins class="diffchange diffchange-inline">Figure 9: </ins>Comparison between the prediction of OCTOPUS and the real protein]]</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>| [[Image:hexa_human_spoctopus_vs_real.png|thumb|Comparison between the prediction of SPOCTOPUS and the real protein]]</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>| [[Image:hexa_human_spoctopus_vs_real.png|thumb|<ins class="diffchange diffchange-inline">Figure 10: </ins>Comparison between the prediction of SPOCTOPUS and the real protein]]</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="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="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>SPOCTOPUS gave us the better result, because SPOCTOPUS <del class="diffchange diffchange-inline">recognices</del> the signal peptide, whereas OCTOPUS predicts a transmembrane helix instead.</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>SPOCTOPUS gave us the better result<ins class="diffchange diffchange-inline"> (Figure 10)</ins>, because SPOCTOPUS <ins class="diffchange diffchange-inline">recognizes</ins> the signal peptide, whereas OCTOPUS predicts a transmembrane helix instead<ins class="diffchange diffchange-inline"> (Figure 9)</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;"><div><br><br></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><br><br></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>Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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>Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></div></td>
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<td colspan="2" class="diff-lineno">Line 176:</td>
<td colspan="2" class="diff-lineno">Line 176:</td>
</tr>
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<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>=== SignalP ===</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>=== SignalP ===</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="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>For our analysis we used the <del class="diffchange diffchange-inline">hidden</del> <del class="diffchange diffchange-inline">markov</del> <del class="diffchange diffchange-inline">model</del> based and also the neuronal network based prediction. <br></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>For our analysis we used the <ins class="diffchange diffchange-inline">Hidden</ins> <ins class="diffchange diffchange-inline">Markov</ins> <ins class="diffchange diffchange-inline">Model</ins> based and also the neuronal network based prediction. <br></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 prediction with the <del class="diffchange diffchange-inline">hidden</del> <del class="diffchange diffchange-inline">markov</del> <del class="diffchange diffchange-inline">model</del> used three different scores. The S-score which is the score for the signal peptide, the C-score which is the score for the <del class="diffchange diffchange-inline">clevage</del> site and the Y-score which is a combination of the S-score and the C-score and is used to predict the cleavage site, because the Y-score is more precise than the C-score.</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 prediction with the <ins class="diffchange diffchange-inline">Hidden</ins> <ins class="diffchange diffchange-inline">Markov</ins> <ins class="diffchange diffchange-inline">Model</ins> used three different scores. The S-score which is the score for the signal peptide, the C-score which is the score for the <ins class="diffchange diffchange-inline">cleavage</ins> site and the Y-score which is a combination of the S-score and the C-score and is used to predict the cleavage site, because the Y-score is more precise than the C-score.</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><br><br></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><br><br></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>'''Result of the neuronal network'''</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>'''Result of the neuronal network'''</div></td>
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<td colspan="2" class="diff-lineno">Line 199:</td>
<td colspan="2" class="diff-lineno">Line 199:</td>
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<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>
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<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>
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<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>'''Result of the <del class="diffchange diffchange-inline">hidden</del> <del class="diffchange diffchange-inline">markov</del> <del class="diffchange diffchange-inline">model</del>'''</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>'''Result of the <ins class="diffchange diffchange-inline">Hidden</ins> <ins class="diffchange diffchange-inline">Markov</ins> <ins class="diffchange diffchange-inline">Model</ins>'''</div></td>
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<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>{| border="1" style="text-align:center; border-spacing:0;"</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>{| border="1" style="text-align:center; border-spacing:0;"</div></td>
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<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>|prediction</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>|prediction</div></td>
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<td colspan="2" class="diff-lineno">Line 216:</td>
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<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>
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<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>
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<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>| [[Image:hexa_human_signalp_nn.png|thumb|Result of the SignalP method based on the neuronal network]]</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>| [[Image:hexa_human_signalp_nn.png|thumb|<ins class="diffchange diffchange-inline">Figure 11: </ins>Result of the SignalP method based on the neuronal network]]</div></td>
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<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>| [[Image:hexa_human_signalp_hmm.png|thumb|Result of the SignalP method based on the hidden markov model]]</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>| [[Image:hexa_human_signalp_hmm.png|thumb|<ins class="diffchange diffchange-inline">Figure 12: </ins>Result of the SignalP method based on the hidden markov model]]</div></td>
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<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>
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<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>
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<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>Both methods predict the same start and end position of the cleavage site and also both methods predict a signal peptide, which is correct because HEXA_HUMAN takes part at the secretory pathway.</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>Both methods<ins class="diffchange diffchange-inline"> (Figure 11 and Figure 12)</ins> predict the same start and end position of the cleavage site and also both methods predict a signal peptide, which is correct because HEXA_HUMAN takes part at the secretory pathway.</div></td>
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<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><br><br></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><br><br></div></td>
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<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>Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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>Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></div></td>
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Link
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Prediction_of_transmembrane_alpha-helices_and_signal_peptides_HEXA_HUMAN&diff=10676&oldid=prev
Link at 13:37, 11 August 2011
2011-08-11T13:37:23Z
<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<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 13:37, 11 August 2011</td>
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<td colspan="2" class="diff-lineno">Line 23:</td>
<td colspan="2" class="diff-lineno">Line 23:</td>
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<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>As you can see above, the TMHMM prediction result is completly right, expect of the signal peptide, which can't be predicted by TMHMM.</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>As you can see above, the TMHMM prediction result is completly right, expect of the signal peptide, which can't be predicted by TMHMM.</div></td>
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<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><br><br></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><br><br></div></td>
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<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>Back to [[<del class="diffchange diffchange-inline">https</del>://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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>Back to [[<ins class="diffchange diffchange-inline">http</ins>://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></div></td>
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<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>=== Phobius and PolyPhobius ===</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>=== Phobius and PolyPhobius ===</div></td>
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<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>
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<td colspan="2" class="diff-lineno">Line 95:</td>
<td colspan="2" class="diff-lineno">Line 95:</td>
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<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 prediction of Phobius is a little bit better than the PolyPhobius prediction, because Phobius predicts the beginning and the end of the signal peptide totally correct, whereas PolyPhobius cuts two residues of the signal peptide.</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 prediction of Phobius is a little bit better than the PolyPhobius prediction, because Phobius predicts the beginning and the end of the signal peptide totally correct, whereas PolyPhobius cuts two residues of the signal peptide.</div></td>
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<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><br><br></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><br><br></div></td>
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<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>Back to [[<del class="diffchange diffchange-inline">https</del>://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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>Back to [[<ins class="diffchange diffchange-inline">http</ins>://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></div></td>
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<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>=== OCTOPUS and SPOCTOPUS ===</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>=== OCTOPUS and SPOCTOPUS ===</div></td>
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<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>
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<td colspan="2" class="diff-lineno">Line 150:</td>
<td colspan="2" class="diff-lineno">Line 150:</td>
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<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>SPOCTOPUS gave us the better result, because SPOCTOPUS recognices the signal peptide, whereas OCTOPUS predicts a transmembrane helix instead.</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>SPOCTOPUS gave us the better result, because SPOCTOPUS recognices the signal peptide, whereas OCTOPUS predicts a transmembrane helix instead.</div></td>
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<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><br><br></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><br><br></div></td>
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<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>Back to [[<del class="diffchange diffchange-inline">https</del>://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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>Back to [[<ins class="diffchange diffchange-inline">http</ins>://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></div></td>
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<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>=== TargetP ===</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>=== TargetP ===</div></td>
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<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><br></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><br></div></td>
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<td colspan="2" class="diff-lineno">Line 173:</td>
<td colspan="2" class="diff-lineno">Line 173:</td>
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<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>TargetP predicts a secretory pathway signal peptide for this protein, which is correct. <br><br></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>TargetP predicts a secretory pathway signal peptide for this protein, which is correct. <br><br></div></td>
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<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><br><br></div></td>
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<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><br><br></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>Back to [[<del class="diffchange diffchange-inline">https</del>://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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>Back to [[<ins class="diffchange diffchange-inline">http</ins>://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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>=== SignalP ===</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>=== SignalP ===</div></td>
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<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>
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<td colspan="2" class="diff-lineno">Line 222:</td>
<td colspan="2" class="diff-lineno">Line 222:</td>
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<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>Both methods predict the same start and end position of the cleavage site and also both methods predict a signal peptide, which is correct because HEXA_HUMAN takes part at the secretory pathway.</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>Both methods predict the same start and end position of the cleavage site and also both methods predict a signal peptide, which is correct because HEXA_HUMAN takes part at the secretory pathway.</div></td>
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<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><br><br></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><br><br></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>Back to [[<del class="diffchange diffchange-inline">https</del>://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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>Back to [[<ins class="diffchange diffchange-inline">http</ins>://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></div></td>
</tr>
</table>
Link
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Prediction_of_transmembrane_alpha-helices_and_signal_peptides_HEXA_HUMAN&diff=10675&oldid=prev
Link at 13:36, 11 August 2011
2011-08-11T13:36:40Z
<p></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 13:36, 11 August 2011</td>
</tr><tr>
<td colspan="2" class="diff-lineno">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</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>=== TMHMM ===</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>=== TMHMM ===</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>First of all, we analysed the protein with TMHMM.</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>[[Image:hexa_human_tmhmm.png|thumb|Prediction of TMHMM for the transmembrane helices of HEXA_HUMAN]]</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>[[Image:hexa_human_tmhmm.png|thumb|Prediction of TMHMM for the transmembrane helices of HEXA_HUMAN]]</div></td>
</tr>
<tr>
<td colspan="2" class="diff-lineno">Line 21:</td>
<td colspan="2" class="diff-lineno">Line 23:</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>As you can see above, the TMHMM prediction result is completly right, expect of the signal peptide, which can't be predicted by TMHMM.</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>As you can see above, the TMHMM prediction result is completly right, expect of the signal peptide, which can't be predicted by TMHMM.</div></td>
</tr>
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<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><br><br></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><br><br></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>Back to [[https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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="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>=== Phobius and PolyPhobius ===</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>=== Phobius and PolyPhobius ===</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>Next, we used Phobius and also PolyPhobius to predict the transmembrane helices and also the signale peptide.</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>[[Image:phobius.png|thumb|Prediction of Phobius for the transmembrane helices and signal peptides of HEXA_HUMAN]]</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>[[Image:phobius.png|thumb|Prediction of Phobius for the transmembrane helices and signal peptides of HEXA_HUMAN]]</div></td>
</tr>
<tr>
<td colspan="2" class="diff-lineno">Line 91:</td>
<td colspan="2" class="diff-lineno">Line 95:</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 prediction of Phobius is a little bit better than the PolyPhobius prediction, because Phobius predicts the beginning and the end of the signal peptide totally correct, whereas PolyPhobius cuts two residues of the signal peptide.</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 prediction of Phobius is a little bit better than the PolyPhobius prediction, because Phobius predicts the beginning and the end of the signal peptide totally correct, whereas PolyPhobius cuts two residues of the signal peptide.</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><br><br></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><br><br></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>Back to [[https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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="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>=== OCTOPUS and SPOCTOPUS ===</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>=== OCTOPUS and SPOCTOPUS ===</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>As next tools we used OCTOPUS and SPOCTOPUS to predict the transmembrane helices and the signal peptide again.</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><br><br></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><br><br></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>[[Image:hexa_human_octopus.png|thumb|Prediction of OCTOPUS for the transmembrane helices of HEXA_HUMAN]]</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>[[Image:hexa_human_octopus.png|thumb|Prediction of OCTOPUS for the transmembrane helices of HEXA_HUMAN]]</div></td>
</tr>
<tr>
<td colspan="2" class="diff-lineno">Line 144:</td>
<td colspan="2" class="diff-lineno">Line 150:</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>SPOCTOPUS gave us the better result, because SPOCTOPUS recognices the signal peptide, whereas OCTOPUS predicts a transmembrane helix instead.</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>SPOCTOPUS gave us the better result, because SPOCTOPUS recognices the signal peptide, whereas OCTOPUS predicts a transmembrane helix instead.</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><br><br></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><br><br></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>Back to [[https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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="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>=== TargetP ===</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>=== TargetP ===</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><br></div></td>
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<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>All of our proteins are proteins from human and archaea, so therefore we only use the non-plant option of TargetP.</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><br><br></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><br><br></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>{| border="1" style="text-align:center; border-spacing:0;"</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>{| border="1" style="text-align:center; border-spacing:0;"</div></td>
</tr>
<tr>
<td colspan="2" class="diff-lineno">Line 165:</td>
<td colspan="2" class="diff-lineno">Line 173:</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>TargetP predicts a secretory pathway signal peptide for this protein, which is correct. <br><br></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>TargetP predicts a secretory pathway signal peptide for this protein, which is correct. <br><br></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><br><br></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><br><br></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>Back to [[https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></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="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>=== SignalP ===</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>=== SignalP ===</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 colspan="2" class="diff-lineno">Line 214:</td>
<td colspan="2" class="diff-lineno">Line 222:</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>Both methods predict the same start and end position of the cleavage site and also both methods predict a signal peptide, which is correct because HEXA_HUMAN takes part at the secretory pathway.</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>Both methods predict the same start and end position of the cleavage site and also both methods predict a signal peptide, which is correct because HEXA_HUMAN takes part at the secretory pathway.</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><br><br></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><br><br></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>Back to [[https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_predictions_HEXA#Prediction_of_transmembrane_alpha-helices_and_signal_peptides sequence-based prediction]]<br><br></div></td>
</tr>
</table>
Link
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Prediction_of_transmembrane_alpha-helices_and_signal_peptides_HEXA_HUMAN&diff=10673&oldid=prev
Link: Created page with "=== TMHMM === Prediction of TMHMM for the transmembrane helices of HEXA_HUMAN {| border="1" style="text-align:center; border-spacing:0;" |-…"
2011-08-11T13:32:19Z
<p>Created page with "=== TMHMM === <a href="/wiki/index.php/File:Hexa_human_tmhmm.png" title="File:Hexa human tmhmm.png">thumb|Prediction of TMHMM for the transmembrane helices of HEXA_HUMAN</a> {| border="1" style="text-align:center; border-spacing:0;" |-…"</p>
<p><b>New page</b></p><div>=== TMHMM ===<br />
<br />
[[Image:hexa_human_tmhmm.png|thumb|Prediction of TMHMM for the transmembrane helices of HEXA_HUMAN]]<br />
<br />
{| border="1" style="text-align:center; border-spacing:0;"<br />
|-<br />
|start position<br />
|end position<br />
|location<br />
|-<br />
|1<br />
|529<br />
|outside<br />
|-<br />
|}<br />
<br />
TMHMM predicts no transmembrane helix at all. The whole protein is located at the extracellular space. To evaluate this result, we compared the data from UniProt with our prediction.<br />
<br />
[[Image:hexa_human_tmhmm_vs_real.png|center|thumb|Comparison between real occuring transmembrane helices and the TMHMM result.]]<br />
<br />
As you can see above, the TMHMM prediction result is completly right, expect of the signal peptide, which can't be predicted by TMHMM.<br />
<br><br><br />
<br />
=== Phobius and PolyPhobius ===<br />
<br />
[[Image:phobius.png|thumb|Prediction of Phobius for the transmembrane helices and signal peptides of HEXA_HUMAN]]<br />
[[Image:polyphobius.png|thumb|Prediction of PolyPhobius for the transmembrane helices and signal peptides of HEXA_HUMAN]]<br />
<br />
{| border="1" style="text-align:center; border-spacing:0;"<br />
!colspan="3"|'''Phobius'''<br />
|colspan="3"|'''PolyPhobius'''<br />
|-<br />
|start position<br />
|end position<br />
|prediction<br />
|start position<br />
|end position<br />
|prediction<br />
|-<br />
!colspan="6" | Signal peptide prediction<br />
|-<br />
|1<br />
|5<br />
|N-Region<br />
|1<br />
|5<br />
|N-Region<br />
|-<br />
|6<br />
|17<br />
|H-Region<br />
|6<br />
|15<br />
|H-Region<br />
|-<br />
|18<br />
|22<br />
|C-Region<br />
|16<br />
|19<br />
|C-Region<br />
|-<br />
!colspan="6" | Summary signal peptide<br />
|-<br />
|1<br />
|22<br />
|Signal Peptide<br />
|1<br />
|19 <br />
|Signal Peptide<br />
|-<br />
!colspan="6" | Transmembrane helices prediction<br />
|-<br />
|23<br />
|529<br />
|outside<br />
|20<br />
|520<br />
|outside<br />
|}<br />
<br />
Both methods don't predict a transmembrane helix, which is correct, because HEXA_HUMAN is located at the lysosmal space.<br />
We compared the results of Phobius and PolyPhobius with the real protein.<br />
<br><br><br />
Comparison with the real structure of the protein:<br />
{|<br />
| [[Image:hexa_phobius_vs_real.png|thumb|Comparison between the prediction of Phobius and the real protein]]<br />
| [[Image:hexa_poly_vs_real.png|thumb|Comparison between the prediction of PolyPhobius and the real protein]]<br />
|}<br />
<br />
The prediction of Phobius is a little bit better than the PolyPhobius prediction, because Phobius predicts the beginning and the end of the signal peptide totally correct, whereas PolyPhobius cuts two residues of the signal peptide.<br />
<br><br><br />
<br />
=== OCTOPUS and SPOCTOPUS ===<br />
<br><br><br />
[[Image:hexa_human_octopus.png|thumb|Prediction of OCTOPUS for the transmembrane helices of HEXA_HUMAN]]<br />
[[Image:hexa_human_spoctopus.png|thumb|Prediction of SPOCTOPUS for the transmembrane helices of HEXA_HUMAN]]<br />
<br />
{| border="1" style="text-align:center; border-spacing:0;"<br />
!colspan="3"|'''OCTOPUS'''<br />
|colspan="3"|'''SPOCTOPUS'''<br />
|-<br />
|start position<br />
|end position<br />
|prediction<br />
|start position<br />
|end position<br />
|prediction<br />
|-<br />
|1<br />
|2<br />
|inside<br />
|1<br />
|6<br />
|N-terminal of a signal peptide<br />
|-<br />
|3<br />
|23<br />
|TM helix<br />
|7<br />
|21<br />
|signal peptide<br />
|-<br />
|24<br />
|529<br />
|outside<br />
|22<br />
|529<br />
|outside<br />
|-<br />
|}<br />
<br />
The results of these two predictions differ. <br />
OCTOPUS predicts a transmembrane helix, whereas SPOCTOPUS predicts at the same location a signal peptide.<br />
<br><br />
To check which method predicted right, we compared the protein and the prediction.<br />
<br><br><br />
Comparison with the real structure of the protein:<br />
{|<br />
| [[Image:hexa_human_octopus_vs_real.png|thumb|Comparison between the prediction of OCTOPUS and the real protein]]<br />
| [[Image:hexa_human_spoctopus_vs_real.png|thumb|Comparison between the prediction of SPOCTOPUS and the real protein]]<br />
|}<br />
<br />
SPOCTOPUS gave us the better result, because SPOCTOPUS recognices the signal peptide, whereas OCTOPUS predicts a transmembrane helix instead.<br />
<br><br><br />
<br />
=== TargetP ===<br />
<br><br><br />
{| border="1" style="text-align:center; border-spacing:0;"<br />
|-<br />
|Location<br />
|Probability<br />
|-<br />
|mitochondrial targeting SP<br />
|0.214<br />
|-<br />
|secretory pathway SP<br />
|0.877<br />
|-<br />
|other<br />
|0.009<br />
|-<br />
|}<br />
<br />
TargetP predicts a secretory pathway signal peptide for this protein, which is correct. <br><br><br />
<br><br><br />
<br />
=== SignalP ===<br />
<br />
For our analysis we used the hidden markov model based and also the neuronal network based prediction. <br><br />
The prediction with the hidden markov model used three different scores. The S-score which is the score for the signal peptide, the C-score which is the score for the clevage site and the Y-score which is a combination of the S-score and the C-score and is used to predict the cleavage site, because the Y-score is more precise than the C-score.<br />
<br><br><br />
'''Result of the neuronal network'''<br />
{| border="1" style="text-align:center; border-spacing:0;"<br />
|colspan="2" | Signal peptide<br />
|colspan="2" | Clevage site<br />
|colspan="1" |<br />
|-<br />
|start position<br />
|end position<br />
|start position<br />
|end position<br />
|prediction<br />
|-<br />
|1<br />
|22<br />
|22<br />
|23<br />
|signal peptide<br />
|-<br />
|}<br />
<br />
'''Result of the hidden markov model'''<br />
{| border="1" style="text-align:center; border-spacing:0;"<br />
|prediction<br />
|signal peptide probability<br />
|signal anchor probability<br />
|cleavage site start<br />
|cleavage site end<br />
|-<br />
|signal peptide<br />
|1.000<br />
|0.000<br />
|22<br />
|23<br />
|-<br />
|}<br />
<br />
{|<br />
| [[Image:hexa_human_signalp_nn.png|thumb|Result of the SignalP method based on the neuronal network]]<br />
| [[Image:hexa_human_signalp_hmm.png|thumb|Result of the SignalP method based on the hidden markov model]]<br />
|}<br />
<br />
Both methods predict the same start and end position of the cleavage site and also both methods predict a signal peptide, which is correct because HEXA_HUMAN takes part at the secretory pathway.<br />
<br><br></div>
Link