Difference between revisions of "Lab Journal - Task 3 (PAH)"
m (→Signal peptides) |
(→Secondary structure) |
||
| Line 1: | Line 1: | ||
== Secondary structure == |
== Secondary structure == |
||
| + | Simple call of reprof: |
||
| + | For P10775 three calls were done. For the first one a FASTA file is used as input, whereas PSSM matrices are delivered for the other two. One created with PSI-Blast against the big80 database the other against swissprot. |
||
| + | *<code> reprof -i <query>.fasta </code> |
||
| + | *<code> reprof -i <query>.pssm </code> |
||
| + | |||
== Disorder == |
== Disorder == |
||
== Transmembrane helices == |
== Transmembrane helices == |
||
Revision as of 12:12, 1 June 2013
Secondary structure
Simple call of reprof: For P10775 three calls were done. For the first one a FASTA file is used as input, whereas PSSM matrices are delivered for the other two. One created with PSI-Blast against the big80 database the other against swissprot.
reprof -i <query>.fastareprof -i <query>.pssm
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.
