Difference between revisions of "Gaucher Task06 Protocol"

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(→‎SNAP)
 
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== Mutation list ==
  +
We need a file "mutations.txt" containing the mutations for using SIFT and SNAP:
  +
H99R
  +
V211I
  +
E150K
  +
L236P
  +
W248R
  +
L509P
  +
W351C
  +
A423D
  +
D482N
  +
R83S
  +
 
== Sources ==
 
== Sources ==
 
You can checkout the git repository containing all relevant data an scripts by:
  
You can checkout the git repository containing all relevant data an scripts by:
Line 24: Line 37:
   
 
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/>
  
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.
   
 
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/>
  
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.
   
 
== PlyPhen2 ==
  
== PlyPhen2 ==
   
−
We used the [http://genetics.bwh.harvard.edu/pph2/ online server of PolyPhen-2].
 +
We used the [http://genetics.bwh.harvard.edu/pph2/ online server of PolyPhen-2]. <br/>
  +
  +
Input: the protein sequence [http://www.uniprot.org/uniprot/P04062.fasta P04062], the position of the mutant, wildtype residue and the mutant. Other setting default.
   
 
== SNAP ==
  
== SNAP ==
  +
  +
The [http://rostlab.org/services/snap/submit web site version of SNAP] seems not work. [https://rostlab.org/owiki/index.php/Snap SNAP] is also installed on the student cluster and should be used command-line only. We need to create our own '~/.snapfunrc' file to point to the correct paths.
  +
vi ~/.snapfunrc
  +
The '~/.snapfunrc' file should have the following contents (<span style="color:red">note that the path to pfam database should be changed compared to the given file '<code>~/[[.snapfunrc]]</code>', otherwise "Failed to open HMM database..." will be reported </span>):
  +
  +
[snapfun]
  +
# snapfun_utildir=path - path to package utilities, default: /usr/share/snapfun
  +
snapfun_utildir=/usr/share/snapfun
  +
# librg_utils_perl=path - path to librg-utils-perl utilities, default: /usr/share/librg-utils-perl
  +
librg_utils_perl=/usr/share/librg-utils-perl
  +
# blastpgp_segfilter=[T|F] - SEG filtering for blastpgpg, untested, default: F
  +
blastpgp_segfilter=F
  +
# blastpgp_processors=int - number of processors to use with blastpgp and hmmpfam, default: 1
  +
blastpgp_processors=1
  +
# hmmpfam executable
  +
hmmpfam=hmm2pfam
  +
# psic matrix
  +
psic_matrix=/usr/share/psic/blosum62_psic.txt
  +
# psic runner
  +
runpsic=/usr/share/rost-runpsic/runNewPSIC.pl
  +
# default mode of the program: [published|optimized|[predictprotein]
  +
mode=optimized
  +
  +
[data]
  +
# swiss_dat=path - location of UniProt/Swiss-Prot dat file
  +
swiss_dat=/mnt/project/pracstrucfunc12/data/swissprot/uniprot_sprot.dat
  +
# db_swiss=path - path to ID index of Swiss-Prot dat file (generated by /usr/share/librg-utils-perl/dbSwiss.pl)
  +
db_swiss=/mnt/project/pracstrucfunc12/data/swissprot/dbswiss
  +
# pfamdata=path - path to pfam database
  +
pfamdata=/mnt/project/pracstrucfunc12/data/pfam_legacy/Pfam_ls
  +
  +
[blast]
  +
# uniref=path - path to comprehensive sequence database (UniRef or equivalent)
  +
uniref=/mnt/project/pracstrucfunc12/data/big/big
  +
# uniref90=path - path to redundancy reduced database (UniRef90 or equivalent)
  +
uniref90=/mnt/project/pracstrucfunc12/data/big/big_80
  +
# swiss=path - path to SwissProt database
  +
swiss=/mnt/project/pracstrucfunc12/data/swissprot/uniprot_sprot
  +
  +
To run SNAP:
  +
snapfun -i P04062.fasta -m mutations.txt -o snapfun_out.out

Latest revision as of 13:12, 18 June 2012

Mutation list

We need a file "mutations.txt" containing the mutations for using SIFT and SNAP: 

H99R
V211I
E150K
L236P
W248R
L509P
W351C
A423D
D482N
R83S

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.

Input: the protein sequence P04062, the position of the mutant, wildtype residue and the mutant. Other setting default.

SNAP

The web site version of SNAP seems not work. SNAP is also installed on the student cluster and should be used command-line only. We need to create our own '~/.snapfunrc' file to point to the correct paths. 

vi ~/.snapfunrc

The '~/.snapfunrc' file should have the following contents (note that the path to pfam database should be changed compared to the given file '~/.snapfunrc', otherwise "Failed to open HMM database..." will be reported ): 

[snapfun]
# snapfun_utildir=path - path to package utilities, default: /usr/share/snapfun
snapfun_utildir=/usr/share/snapfun
# librg_utils_perl=path - path to librg-utils-perl utilities, default: /usr/share/librg-utils-perl
librg_utils_perl=/usr/share/librg-utils-perl
# blastpgp_segfilter=[T|F] - SEG filtering for blastpgpg, untested, default: F
blastpgp_segfilter=F
# blastpgp_processors=int - number of processors to use with blastpgp and hmmpfam, default: 1
blastpgp_processors=1
# hmmpfam executable
hmmpfam=hmm2pfam
# psic matrix
psic_matrix=/usr/share/psic/blosum62_psic.txt
# psic runner
runpsic=/usr/share/rost-runpsic/runNewPSIC.pl
# default mode of the program: [published|optimized|[predictprotein]
mode=optimized

[data]
# swiss_dat=path - location of UniProt/Swiss-Prot dat file
swiss_dat=/mnt/project/pracstrucfunc12/data/swissprot/uniprot_sprot.dat
# db_swiss=path - path to ID index of Swiss-Prot dat file (generated by /usr/share/librg-utils-perl/dbSwiss.pl)
db_swiss=/mnt/project/pracstrucfunc12/data/swissprot/dbswiss
# pfamdata=path - path to pfam database
pfamdata=/mnt/project/pracstrucfunc12/data/pfam_legacy/Pfam_ls

[blast]
# uniref=path - path to comprehensive sequence database (UniRef or equivalent)
uniref=/mnt/project/pracstrucfunc12/data/big/big
# uniref90=path - path to redundancy reduced database (UniRef90 or equivalent)
uniref90=/mnt/project/pracstrucfunc12/data/big/big_80
# swiss=path - path to SwissProt database
swiss=/mnt/project/pracstrucfunc12/data/swissprot/uniprot_sprot

To run SNAP: 

snapfun -i P04062.fasta -m mutations.txt -o snapfun_out.out
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