Gaucher Task05 Protocol

From Bioinformatikpedia


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 highlights the mutated residues with difference colors, we wrote the perl scripts scripts/

scripts/ -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/ which creates a pml file for pymol.

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

data/2nt0_A.pdb is the PDB structure, maps residue positions 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 was created based on the HHsearch alignment:

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