Difference between revisions of "Lab Journal - Task 3 (PAH)"
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== Transmembrane helices == |
== Transmembrane helices == |
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== Signal peptides == |
== Signal peptides == |
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| + | We tried two different parameters for our predictions:<br> |
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| − | Signal peptides are sequences of amino acids in a protein that determine the pathway of the protein in the cell to its destination.<br> |
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| − | On the server version 3.0 of SignalP predictions is installed. We tried two different parameters for our predictions:<br> |
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First we simple run SignalP without any constraints. The only thing, which has to be stated is ''-t euk'' as all four sequences are eukaryotic. Otherwise SignalP only would accept Gran+ or Gran-. |
First we simple run SignalP without any constraints. The only thing, which has to be stated is ''-t euk'' as all four sequences are eukaryotic. Otherwise SignalP only would accept Gran+ or Gran-. |
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-o can be set, so the output is written automatically in output.txt or it can be set with '>'. |
-o can be set, so the output is written automatically in output.txt or it can be set with '>'. |
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| − | + | <code>signalp -t euk <UniprotID>.fasta > <UniprotID>_output.out </code> |
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In our second run we choose only the N-terminal with 70 residues as it is recommended in the manual page of SignalP to avoid false positives. |
In our second run we choose only the N-terminal with 70 residues as it is recommended in the manual page of SignalP to avoid false positives. |
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| − | + | <code>signalp -trunc 70 -t euk <UniprotID>.fasta > <UniprotID>_trunc.out</code> |
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| + | In our case there are only few differences between the runs for the whole sequence or only the N-terminal. For example for the whole sequence the NN result of P47863 gives also a YES for C and not only for max.S. <xr id="signalp"/> shows the results of the N-terminal run only. |
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Revision as of 10:59, 1 June 2013
Secondary structure
Disorder
Transmembrane helices
Signal peptides
We tried two different parameters for our predictions:
First we simple run SignalP without any constraints. The only thing, which has to be stated is -t euk as all four sequences are eukaryotic. Otherwise SignalP only would accept Gran+ or Gran-.
-o can be set, so the output is written automatically in output.txt or it can be set with '>'.
signalp -t euk <UniprotID>.fasta > <UniprotID>_output.out
In our second run we choose only the N-terminal with 70 residues as it is recommended in the manual page of SignalP to avoid false positives.
signalp -trunc 70 -t euk <UniprotID>.fasta > <UniprotID>_trunc.out
In our case there are only few differences between the runs for the whole sequence or only the N-terminal. For example for the whole sequence the NN result of P47863 gives also a YES for C and not only for max.S. <xr id="signalp"/> shows the results of the N-terminal run only.
