Difference between revisions of "Gaucher Task06 Protocol"

Revision as of 13:42, 14 June 2012

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

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

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 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

@@ Line 11: / Line 11: @@
 </pre>
-We used the script <tt>alignhits.pl</hh> from the HHsuite for filtering out the most similar hits from the PSI-BLAST result file:
+We used the script <tt>alignhits.pl</tt> from the HHsuite for filtering out the most similar hits from the PSI-BLAST result file:
 <pre>
 alignhits.pl -Q data/P04062.seq -qsc 1.5 pssm/all/P04062.bla pssm/best/P04062.psi