Gaucher Task05 Protocol

Sources

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

git clone /mnt/home/student/angermue/mp/tasks/task05

Visualising mutated sequence residues

For creating the sequence maps which highlight the mutated residues by difference colors, we wrote the perl scripts scripts/color_seq.pl

scripts/color_seq.pl -i data/P04062.seq -r dbsnp/dbsnp_m.dat dbsnp/dbsnp_s.dat -l Wildtype Missense Synonymous --show

Visualising mutations in the PDB structures

For visualising genetic variants in PDB structures, we wrote scripts/color_pdb.pl which creates a pml file for pymol.

scripts/color_pdb.pl -p data/2nt0_A.pdb -m P04062_2nt0_a.map -r dbsnp/dbsnp_m.dat dbsnp/dbsnp_s.dat -o dbsnp/dbsnp.pml

data/2nt0_A.pdb is the PDB structure, P04062_2nt0_a.map maps residue postions from data/P04062.seq to data/2nt0_a.pdb and the files specified by -r contain the residues to be visualised. The output file dbsnp/dbsnp.pml can than be opened with pymol:

pymol dbsnp/dbsnp.pml

The mapping file P04062_2nt0_a.map was created based on the HHsearch alignment:

scripts/hhsearch_map.pl -i data/P04062.hhr -n 1