Difference between revisions of "Gaucher Task05 Protocol"
From Bioinformatikpedia
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== Visualising mutated sequence residues == |
== Visualising mutated sequence residues == |
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| − | For creating the sequence maps which |
+ | For creating the sequence maps which highlights the mutated residues with difference colors, we wrote the perl scripts <tt>scripts/color_seq.pl</tt> |
<pre> |
<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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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 |
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> |
</pre> |
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| − | <tt>data/2nt0_A.pdb</tt> is the PDB structure, <tt>P04062_2nt0_a.map</tt> maps residue |
+ | <tt>data/2nt0_A.pdb</tt> is the PDB structure, <tt>P04062_2nt0_a.map</tt> maps residue positions 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: |
<pre> |
<pre> |
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pymol dbsnp/dbsnp.pml |
pymol dbsnp/dbsnp.pml |
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Latest revision as of 15:28, 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 highlights the mutated residues with 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 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 P04062_2nt0_a.map was created based on the HHsearch alignment:
scripts/hhsearch_map.pl -i data/P04062.hhr -n 1
