Difference between revisions of "Lab Journal - Task 3 (PAH)"
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We tried two different parameters for our predictions:<br> |
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 '>'.<br> |
| − | <code>signalp -t euk <UniprotID>.fasta > <UniprotID>_output.out </code> |
+ | <code>signalp -t euk <UniprotID>.fasta > <UniprotID>_output.out </code><br> |
| − | 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. <br> |
| − | <code>signalp -trunc 70 -t euk <UniprotID>.fasta > <UniprotID>_trunc.out</code> |
+ | <code>signalp -trunc 70 -t euk <UniprotID>.fasta > <UniprotID>_trunc.out</code><br> |
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. [[Sequence-based predictions (Phenylketonuria) #Signal peptides|Table 15]] shows the results of the N-terminal run only. |
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. [[Sequence-based predictions (Phenylketonuria) #Signal peptides|Table 15]] shows the results of the N-terminal run only. |
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Revision as of 11:05, 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. Table 15 shows the results of the N-terminal run only.
