Difference between revisions of "Gaucher Task05 Protocol"
From Bioinformatikpedia
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<pre> |
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scripts/color_seq.pl -i data/P04062.seq -r dbsnp/dbsnp_m.dat dbsnp/dbsnp_s.dat -l Wildtype Missense Synonymous --show |
scripts/color_seq.pl -i data/P04062.seq -r dbsnp/dbsnp_m.dat dbsnp/dbsnp_s.dat -l Wildtype Missense Synonymous --show |
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| + | </pre> |
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| + | |||
| + | == Visualising mutations in the PDB structures == |
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| + | For visualising genetic variants in PDB structures, we wrote <tt>scripts/color_pdb.pl</tt> which creates a pml file for pymol. |
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| + | <pre> |
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| + | 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 |
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| + | </pre> |
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| + | <tt>data/2nt0_A.pdb</tt> is the PDB structure, <tt>P04062_2nt0_a.map</tt> maps residue postions from <tt>data/P04062.seq</tt> to <tt>data/2nt0_a.pdb</tt> and the files specified by <tt>-r</tt> contain the residues to be visualised. The output file <tt>dbsnp/dbsnp.pml</tt> can than be opened with pymol: |
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| + | <pre> |
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| + | pymol dbsnp/dbsnp.pml |
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| + | </pre> |
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| + | The mapping file <tt>P04062_2nt0_a.map</tt> was created based on the HHsearch alignment: |
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| + | <pre> |
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| + | scripts/hhsearch_map.pl -i data/P04062.hhr -n 1 |
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</pre> |
</pre> |
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Revision as of 16:27, 10 June 2012
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
