View source for Lab Journal - Task 3 (PAH)

== 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. PSI-Blast is used with the same parameter like in Task2 with two iterations and an e-value cutoff of 10e-10(for big80: <code>blastpgp -i /mnt/home/student/waldraffs/Masterpraktikum/Task3/secondary_structure/<UniprotID>.fasta -d /mnt/project/rost_db/data/big/big_80 -j 2 -h 10e-10 -b 2000 -v 2000 -o check_out_files/<UniprotID>.out -Q swiss_matrix_<UniprotID>.pssm </code>, for swissprot only the database is changed: <code>-d /mnt/project/pracstrucfunc13/data/swissprot/uniprot_sprot)</code>.
*<code> reprof -i <query>.fasta </code>
*<code> reprof -i <query>.pssm </code>

== Disorder ==
== Transmembrane helices ==
== Signal peptides ==
We tried two different parameters for our predictions:<br>
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 '>'.<br>
<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. <br>
<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.