Difference between revisions of "Gaucher Task06 Protocol"
From Bioinformatikpedia
(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…") |
|||
| Line 9: | Line 9: | ||
<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 |
||
| + | </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: |
||
| + | <pre> |
||
| + | alignhits.pl -Q data/P04062.seq -qsc 1.5 pssm/all/P04062.bla pssm/best/P04062.psi |
||
| + | </pre> |
||
| + | |||
| + | The PSSM for the resulting PSI-BLAST alignment was computed as follows: |
||
| + | <pre> |
||
| + | 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
