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 swissprot: blastpgp -i /mnt/home/student/waldraffs/Masterpraktikum/Task3/secondary_structure/<UniprotID>.fasta -d /mnt/project/pracstrucfunc13/data/swissprot/uniprot_sprot -j 2 -h 10e-10 -b 2000 -v 2000 -o check_out_files/<UniprotID>.out -Q swiss_matrix_<UniprotID>.pssm , big80 -d /mnt/project/rost_db/data/big/big_80).

• reprof -i <query>.fasta
• reprof -i <query>.pssm

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.