Difference between revisions of "Gaucher Task05 Protocol"

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== Visualising mutated sequence residues ==
 
== Visualising mutated sequence residues ==
For creating the sequence maps which highlight the mutated residues by difference colors, we wrote the perl scripts <tt>scripts/color_seq.pl</tt>
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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>
 
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>
  +
  +
== Visualising mutations in the PDB structures ==
  +
For visualising genetic variants in PDB structures, we wrote <tt>scripts/color_pdb.pl</tt> which creates a pml file for pymol.
  +
<pre>
  +
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 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>
  +
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:
  +
<pre>
  +
scripts/hhsearch_map.pl -i data/P04062.hhr -n 1
 
</pre>
 
</pre>

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