Difference between revisions of "Gaucher Task06 Protocol"
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== SIFT == |
== SIFT == |
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| − | We used the [http://sift.jcvi.org/www/SIFT_seq_submit2.html online server of SIFT]. It took a little bit long (10-15 min) because they have to search for the related sequences in database. |
+ | We used the [http://sift.jcvi.org/www/SIFT_seq_submit2.html online server of SIFT]. It took a little bit long (10-15 min) because they have to search for the related sequences in database.<br/> |
Input: the protein sequence [http://www.uniprot.org/uniprot/P04062.fasta P04062], the list of Mutations. Other setting default. |
Input: the protein sequence [http://www.uniprot.org/uniprot/P04062.fasta P04062], the list of Mutations. Other setting default. |
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| − | Alternatively, the [http://sift.jcvi.org/www/SIFT_BLink_submit.html online server of SIFT Blink] was used. The predictions there are based on pre-computed BLAST searches, therefore are returned almost immediately. For SIFT Blink, we should provide the corresponding NCBI GI number ([http://www.ncbi.nlm.nih.gov/protein/CAI95090.1 66347912]) for our protein (UniProt id: [http://www.uniprot.org/uniprot/P04062 P04062]). |
+ | Alternatively, the [http://sift.jcvi.org/www/SIFT_BLink_submit.html online server of SIFT Blink] was used. The predictions there are based on pre-computed BLAST searches, therefore are returned almost immediately. For SIFT Blink, we should provide the corresponding NCBI GI number ([http://www.ncbi.nlm.nih.gov/protein/CAI95090.1 66347912]) for our protein (UniProt id: [http://www.uniprot.org/uniprot/P04062 P04062]).<br/> |
Input: the corresponding NCBI GI number ([http://www.ncbi.nlm.nih.gov/protein/CAI95090.1 66347912]), the list of Mutations. Other setting default. |
Input: the corresponding NCBI GI number ([http://www.ncbi.nlm.nih.gov/protein/CAI95090.1 66347912]), the list of Mutations. Other setting default. |
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Revision as of 20:31, 16 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
We used the online server of SIFT. It took a little bit long (10-15 min) because they have to search for the related sequences in database.
Input: the protein sequence P04062, the list of Mutations. Other setting default.
Alternatively, the online server of SIFT Blink was used. The predictions there are based on pre-computed BLAST searches, therefore are returned almost immediately. For SIFT Blink, we should provide the corresponding NCBI GI number (66347912) for our protein (UniProt id: P04062).
Input: the corresponding NCBI GI number (66347912), the list of Mutations. Other setting default.
PlyPhen2
We used the online server of PolyPhen-2.
