Difference between revisions of "Gaucher Task06 Protocol"

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(Created page with "== Sources == You can checkout the git repository containing all relevant data an scripts by: <pre> git clone /mnt/home/student/angermue/mp/tasks/task06 </pre> == PSSM == We cr…")
 
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<pre>
 
<pre>
 
blastpgp -i data/P04062.seq -d $NR -j 5 -h 1e-3 -b 1000 -o pssm/all/P04062.bla -Q pssm/all/P04062.pssm
 
blastpgp -i data/P04062.seq -d $NR -j 5 -h 1e-3 -b 1000 -o pssm/all/P04062.bla -Q pssm/all/P04062.pssm
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</pre>
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We used the script <tt>alignhits.pl</hh> from the HHsuite for filtering out the most similar hits from the PSI-BLAST result file:
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<pre>
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alignhits.pl -Q data/P04062.seq -qsc 1.5 pssm/all/P04062.bla pssm/best/P04062.psi
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</pre>
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The PSSM for the resulting PSI-BLAST alignment was computed as follows:
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<pre>
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blastpgp -i data/P04062.seq -B pssm/best/P04062.psi -d $DUMMY -j 0 -Q pssm/best/P04062.pssm
 
</pre>
 
</pre>

Revision as of 13:42, 14 June 2012

Sources

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

git clone /mnt/home/student/angermue/mp/tasks/task06

PSSM

We created the PSSM as follows:

blastpgp -i data/P04062.seq -d $NR -j 5 -h 1e-3 -b 1000 -o pssm/all/P04062.bla -Q pssm/all/P04062.pssm

We used the script alignhits.pl</hh> from the HHsuite for filtering out the most similar hits from the PSI-BLAST result file:

alignhits.pl -Q data/P04062.seq -qsc 1.5 pssm/all/P04062.bla pssm/best/P04062.psi

The PSSM for the resulting PSI-BLAST alignment was computed as follows:

blastpgp -i data/P04062.seq -B pssm/best/P04062.psi -d $DUMMY -j 0 -Q pssm/best/P04062.pssm