Gaucher Task06 Protocol

Sources

You can checkout the git repository containing all relevant data an scripts by:

git clone /mnt/home/student/angermue/mp/tasks/task06

PSSM

We created the PSSM as follows:

blastpgp -i data/P04062.seq -d $NR -j 5 -h 1e-3 -b 1000 -o pssm/all/P04062.bla -Q pssm/all/P04062.pssm

We used the script alignhits.pl from the HHsuite for filtering out the most similar hits from the PSI-BLAST result file:

alignhits.pl -Q data/P04062.seq -qsc 1.5 pssm/all/P04062.bla pssm/best/P04062.psi

The PSSM for the resulting PSI-BLAST alignment was computed as follows:

blastpgp -i data/P04062.seq -B pssm/best/P04062.psi -d $DUMMY -j 0 -Q pssm/best/P04062.pssm

SIFT

We used the online server of SIFT. It took a little bit long (10-15 min) because they have to search for the related sequences in database.

Input: the protein sequence P04062, the list of Mutations. Other setting default.

Alternatively, the online server of SIFT Blink was used. The predictions there are based on pre-computed BLAST searches, therefore are returned almost immediately. For SIFT Blink, we should provide the corresponding NCBI GI number (66347912) for our protein (UniProt id: P04062).

Input: the corresponding NCBI GI number (66347912), the list of Mutations. Other setting default.

PlyPhen2

We used the online server of PolyPhen-2.

Input: the protein sequence P04062, the position of the mutant, wildtype residue and the mutant. Other setting default.