Difference between revisions of "Gaucher Task06 Protocol"
From Bioinformatikpedia
(→SIFT) |
|||
| Line 22: | Line 22: | ||
== SIFT == |
== SIFT == |
||
| + | |||
| + | use the [http://sift.jcvi.org/www/SIFT_seq_submit2.html online server of SIFT]. |
||
== PlyPhen2 == |
== PlyPhen2 == |
||
Revision as of 19:09, 15 June 2012
Contents
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 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
SIFT
use the online server of SIFT.
