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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| − | [[Lab Journal - Task 3 (PAH) #Signal peptides|Lab journal]] <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> |
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> |
On the server version 3.0 of SignalP predictions is installed. We tried two different parameters for our predictions:<br> |
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Revision as of 11:58, 1 June 2013
Secondary structure
Disorder
Transmembrane helices
Signal peptides
Signal peptides are sequences of amino acids in a protein that determine the pathway of the protein in the cell to its destination.
On the server version 3.0 of SignalP predictions is installed. 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
