Difference between revisions of "Prediction of transmembrane alpha-helices and signal peptides HEXA HUMAN"

From Bioinformatikpedia
 
Line 3: Line 3:
 
First of all, we analysed the protein with TMHMM.
 
First of all, we analysed the protein with TMHMM.
   
[[Image:hexa_human_tmhmm.png|thumb|Prediction of TMHMM for the transmembrane helices of HEXA_HUMAN]]
+
[[Image:hexa_human_tmhmm.png|thumb|Figure 1: Prediction of TMHMM for the transmembrane helices of HEXA_HUMAN]]
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
Line 17: Line 17:
 
|}
 
|}
   
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.
+
TMHMM predicts no transmembrane helix at all, which can be seen on Figure 1. The whole protein is located at the extracellular space. To evaluate this result, we compared the data from [[http://www.uniprot.org/ UniProt]] with our prediction.
   
[[Image:hexa_human_tmhmm_vs_real.png|center|thumb|Comparison between real occuring transmembrane helices and the TMHMM result.]]
+
[[Image:hexa_human_tmhmm_vs_real.png|center|thumb|Figure 2: Comparison between real occurring transmembrane helices and the TMHMM result.]]
   
As you can see above, the TMHMM prediction result is completly right, expect of the signal peptide, which can't be predicted by TMHMM.
+
As you can see above (Figure 2), the TMHMM prediction result is completely right, expect of the signal peptide, which can't be predicted by TMHMM.
 
<br><br>
 
<br><br>
 
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>
 
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>
 
=== Phobius and PolyPhobius ===
 
=== Phobius and PolyPhobius ===
   
Next, we used Phobius and also PolyPhobius to predict the transmembrane helices and also the signale peptide.
+
Next, we used Phobius and also PolyPhobius to predict the transmembrane helices and also the signal peptide.
   
[[Image:phobius.png|thumb|Prediction of Phobius for the transmembrane helices and signal peptides of HEXA_HUMAN]]
+
[[Image:phobius.png|thumb|Figure 3: Prediction of Phobius for the transmembrane helices and signal peptides of HEXA_HUMAN]]
[[Image:polyphobius.png|thumb|Prediction of PolyPhobius for the transmembrane helices and signal peptides of HEXA_HUMAN]]
+
[[Image:polyphobius.png|thumb|Figure 4: Prediction of PolyPhobius for the transmembrane helices and signal peptides of HEXA_HUMAN]]
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
Line 84: Line 84:
 
|}
 
|}
   
Both methods don't predict a transmembrane helix, which is correct, because HEXA_HUMAN is located at the lysosmal space.
+
Both methods do not predict a transmembrane helix (compare Figure 3 and Figure 4), which is correct, because HEXA_HUMAN is located at the lysosmal space.
 
We compared the results of Phobius and PolyPhobius with the real protein.
 
We compared the results of Phobius and PolyPhobius with the real protein.
 
<br><br>
 
<br><br>
 
Comparison with the real structure of the protein:
 
Comparison with the real structure of the protein:
 
{|
 
{|
| [[Image:hexa_phobius_vs_real.png|thumb|Comparison between the prediction of Phobius and the real protein]]
+
| [[Image:hexa_phobius_vs_real.png|thumb|Figure 5: Comparison between the prediction of Phobius and the real protein]]
| [[Image:hexa_poly_vs_real.png|thumb|Comparison between the prediction of PolyPhobius and the real protein]]
+
| [[Image:hexa_poly_vs_real.png|thumb|Figure 6: Comparison between the prediction of PolyPhobius and the real protein]]
 
|}
 
|}
   
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.
+
The prediction of Phobius (Figure 5) is a little bit better than the PolyPhobius prediction (Figure 6), 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>
 
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>
 
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>
Line 100: Line 100:
 
As next tools we used OCTOPUS and SPOCTOPUS to predict the transmembrane helices and the signal peptide again.
 
As next tools we used OCTOPUS and SPOCTOPUS to predict the transmembrane helices and the signal peptide again.
 
<br><br>
 
<br><br>
[[Image:hexa_human_octopus.png|thumb|Prediction of OCTOPUS for the transmembrane helices of HEXA_HUMAN]]
+
[[Image:hexa_human_octopus.png|thumb|Figure 7: Prediction of OCTOPUS for the transmembrane helices of HEXA_HUMAN]]
[[Image:hexa_human_spoctopus.png|thumb|Prediction of SPOCTOPUS for the transmembrane helices of HEXA_HUMAN]]
+
[[Image:hexa_human_spoctopus.png|thumb|Figure 8: Prediction of SPOCTOPUS for the transmembrane helices of HEXA_HUMAN]]
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
Line 138: Line 138:
   
 
The results of these two predictions differ.
 
The results of these two predictions differ.
OCTOPUS predicts a transmembrane helix, whereas SPOCTOPUS predicts at the same location a signal peptide.
+
OCTOPUS predicts a transmembrane helix (Figure 7), whereas SPOCTOPUS predicts at the same location a signal peptide (Figure 8).
 
<br>
 
<br>
 
To check which method predicted right, we compared the protein and the prediction.
 
To check which method predicted right, we compared the protein and the prediction.
Line 144: Line 144:
 
Comparison with the real structure of the protein:
 
Comparison with the real structure of the protein:
 
{|
 
{|
| [[Image:hexa_human_octopus_vs_real.png|thumb|Comparison between the prediction of OCTOPUS and the real protein]]
+
| [[Image:hexa_human_octopus_vs_real.png|thumb|Figure 9: Comparison between the prediction of OCTOPUS and the real protein]]
| [[Image:hexa_human_spoctopus_vs_real.png|thumb|Comparison between the prediction of SPOCTOPUS and the real protein]]
+
| [[Image:hexa_human_spoctopus_vs_real.png|thumb|Figure 10: Comparison between the prediction of SPOCTOPUS and the real protein]]
 
|}
 
|}
   
SPOCTOPUS gave us the better result, because SPOCTOPUS recognices the signal peptide, whereas OCTOPUS predicts a transmembrane helix instead.
+
SPOCTOPUS gave us the better result (Figure 10), because SPOCTOPUS recognizes the signal peptide, whereas OCTOPUS predicts a transmembrane helix instead (Figure 9).
 
<br><br>
 
<br><br>
 
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>
 
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>
Line 176: Line 176:
 
=== SignalP ===
 
=== SignalP ===
   
For our analysis we used the hidden markov model based and also the neuronal network based prediction. <br>
+
For our analysis we used the Hidden Markov Model based and also the neuronal network based prediction. <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.
+
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 cleavage 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'''
 
'''Result of the neuronal network'''
Line 199: Line 199:
 
|}
 
|}
   
'''Result of the hidden markov model'''
+
'''Result of the Hidden Markov Model'''
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
 
|prediction
 
|prediction
Line 216: Line 216:
   
 
{|
 
{|
| [[Image:hexa_human_signalp_nn.png|thumb|Result of the SignalP method based on the neuronal network]]
+
| [[Image:hexa_human_signalp_nn.png|thumb|Figure 11: Result of the SignalP method based on the neuronal network]]
| [[Image:hexa_human_signalp_hmm.png|thumb|Result of the SignalP method based on the hidden markov model]]
+
| [[Image:hexa_human_signalp_hmm.png|thumb|Figure 12: Result of the SignalP method based on the hidden markov model]]
 
|}
 
|}
   
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.
+
Both methods (Figure 11 and Figure 12) 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><br>
 
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>
 
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>

Latest revision as of 23:03, 30 August 2011

TMHMM

First of all, we analysed the protein with TMHMM.

Figure 1: Prediction of TMHMM for the transmembrane helices of HEXA_HUMAN
start position end position location
1 529 outside

TMHMM predicts no transmembrane helix at all, which can be seen on Figure 1. The whole protein is located at the extracellular space. To evaluate this result, we compared the data from [UniProt] with our prediction.

Figure 2: Comparison between real occurring transmembrane helices and the TMHMM result.

As you can see above (Figure 2), the TMHMM prediction result is completely right, expect of the signal peptide, which can't be predicted by TMHMM.

Back to [sequence-based prediction]

Phobius and PolyPhobius

Next, we used Phobius and also PolyPhobius to predict the transmembrane helices and also the signal peptide.

Figure 3: Prediction of Phobius for the transmembrane helices and signal peptides of HEXA_HUMAN
Figure 4: Prediction of PolyPhobius for the transmembrane helices and signal peptides of HEXA_HUMAN
Phobius PolyPhobius
start position end position prediction start position end position prediction
Signal peptide prediction
1 5 N-Region 1 5 N-Region
6 17 H-Region 6 15 H-Region
18 22 C-Region 16 19 C-Region
Summary signal peptide
1 22 Signal Peptide 1 19 Signal Peptide
Transmembrane helices prediction
23 529 outside 20 520 outside

Both methods do not predict a transmembrane helix (compare Figure 3 and Figure 4), which is correct, because HEXA_HUMAN is located at the lysosmal space. We compared the results of Phobius and PolyPhobius with the real protein.

Comparison with the real structure of the protein:

Figure 5: Comparison between the prediction of Phobius and the real protein
Figure 6: Comparison between the prediction of PolyPhobius and the real protein

The prediction of Phobius (Figure 5) is a little bit better than the PolyPhobius prediction (Figure 6), because Phobius predicts the beginning and the end of the signal peptide totally correct, whereas PolyPhobius cuts two residues of the signal peptide.

Back to [sequence-based prediction]

OCTOPUS and SPOCTOPUS

As next tools we used OCTOPUS and SPOCTOPUS to predict the transmembrane helices and the signal peptide again.

Figure 7: Prediction of OCTOPUS for the transmembrane helices of HEXA_HUMAN
Figure 8: Prediction of SPOCTOPUS for the transmembrane helices of HEXA_HUMAN
OCTOPUS SPOCTOPUS
start position end position prediction start position end position prediction
1 2 inside 1 6 N-terminal of a signal peptide
3 23 TM helix 7 21 signal peptide
24 529 outside 22 529 outside

The results of these two predictions differ. OCTOPUS predicts a transmembrane helix (Figure 7), whereas SPOCTOPUS predicts at the same location a signal peptide (Figure 8).
To check which method predicted right, we compared the protein and the prediction.

Comparison with the real structure of the protein:

Figure 9: Comparison between the prediction of OCTOPUS and the real protein
Figure 10: Comparison between the prediction of SPOCTOPUS and the real protein

SPOCTOPUS gave us the better result (Figure 10), because SPOCTOPUS recognizes the signal peptide, whereas OCTOPUS predicts a transmembrane helix instead (Figure 9).

Back to [sequence-based prediction]

TargetP


All of our proteins are proteins from human and archaea, so therefore we only use the non-plant option of TargetP.

Location Probability
mitochondrial targeting SP 0.214
secretory pathway SP 0.877
other 0.009

TargetP predicts a secretory pathway signal peptide for this protein, which is correct.



Back to [sequence-based prediction]

SignalP

For our analysis we used the Hidden Markov Model based and also the neuronal network based prediction.
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 cleavage 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.

Result of the neuronal network

Signal peptide Clevage site
start position end position start position end position prediction
1 22 22 23 signal peptide

Result of the Hidden Markov Model

prediction signal peptide probability signal anchor probability cleavage site start cleavage site end
signal peptide 1.000 0.000 22 23
Figure 11: Result of the SignalP method based on the neuronal network
Figure 12: Result of the SignalP method based on the hidden markov model

Both methods (Figure 11 and Figure 12) 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.

Back to [sequence-based prediction]