Difference between revisions of "Protocol"
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| <tt> eval.pl </tt> || Calculates the precision, sensitivity, and specificity given a set of predicted residues, reference residues and the length of the protein. |
| <tt> eval.pl </tt> || Calculates the precision, sensitivity, and specificity given a set of predicted residues, reference residues and the length of the protein. |
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+ | == Transmembrane helices == |
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+ | |||
+ | At first, get all the sequences from Uniprot: |
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+ | |||
+ | wget http://www.uniprot.org/uniprot/P04062.fasta |
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+ | wget http://www.uniprot.org/uniprot/P35462.fasta |
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+ | wget http://www.uniprot.org/uniprot/Q9YDF8.fasta |
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+ | wget http://www.uniprot.org/uniprot/P47863.fasta |
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+ | |||
+ | Then execute the following bash shell script to do prediction: |
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+ | |||
+ | #!/bin/bash |
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+ | #$ -S /bin/sh |
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+ | IN=/mnt/project/pracstrucfunc12/data/index_pp/uniprot_sprot.idx |
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+ | DB=/mnt/project/pracstrucfunc12/data/swissprot/uniprot_sprot |
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+ | PATH=$PATH:/mnt/project/pracstrucfunc12/polyphobius/ |
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+ | export PATH |
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+ | |||
+ | mkdir -p output/ |
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+ | for file in `ls | grep ".fasta"`; do |
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+ | `perl /mnt/project/pracstrucfunc12/polyphobius/blastget -db $DB -ix $IN $file > output/$file.blast` |
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+ | wait |
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+ | `/mnt/opt/T-Coffee/bin/kalign -f fasta -input output/$file.blast -output output/$file.msa` |
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+ | wait |
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+ | `perl /mnt/project/pracstrucfunc12/polyphobius/jphobius -poly output/$file.msa &> output/$file.phob` |
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+ | wait |
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+ | done |
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+ | |||
+ | == Signal peptides == |
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+ | The [http://www.cbs.dtu.dk/services/SignalP/ SignalP] server with version 4.0 was used. |
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+ | |||
+ | == GO terms == |
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+ | |||
+ | To predict GO terms, the online server of [http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar GOPET] and [http://www.cbs.dtu.dk/services/ProtFun/ ProtFun2.0] were used. To check the pfam family, [http://pfam.sanger.ac.uk/ Pfam] was used. |
Latest revision as of 20:39, 21 May 2012
Contents
Secondary structure
Sources
The data and scripts we used can be found in /mnt/home/student/angermue/mp/tasks/task03/ss
DSSP assignment
We simply used the DSSP server to get the DSSP secondary structure assignments.
PSIPRED
For calling PSIPRED, we adjusted the script runpsipred of the PSIPRED package. Three rounds PSI-BLAST were carried out to build the PSI-BLAST profile which is used as input of PSIPRED.
Reprof
We called the pre-installed Reprof program by reprof -i FASTA-SEQUENCE -o OUTPUT-FILE.
Further scripts
ss_format.pl | Converts the output of DSSP, PSIPRED, or Reprof into a common output format with secondary structure states H, E, C. |
ss_eval.pl | Takes a reference and further ss_format.pl formatted files which are to be evaluated. |
ss_viz.pl | Visualizes several ss_format.pl formatted predictions- |
Disorder
Sources
The data and scripts we used can be found in /mnt/home/student/angermue/mp/tasks/task03/disorder
IUPred
We called IUPred by:
iupred SEQ-FILE long
Further scripts
eval.pl | Calculates the precision, sensitivity, and specificity given a set of predicted residues, reference residues and the length of the protein. |
Transmembrane helices
At first, get all the sequences from Uniprot:
wget http://www.uniprot.org/uniprot/P04062.fasta wget http://www.uniprot.org/uniprot/P35462.fasta wget http://www.uniprot.org/uniprot/Q9YDF8.fasta wget http://www.uniprot.org/uniprot/P47863.fasta
Then execute the following bash shell script to do prediction:
#!/bin/bash #$ -S /bin/sh IN=/mnt/project/pracstrucfunc12/data/index_pp/uniprot_sprot.idx DB=/mnt/project/pracstrucfunc12/data/swissprot/uniprot_sprot PATH=$PATH:/mnt/project/pracstrucfunc12/polyphobius/ export PATH mkdir -p output/ for file in `ls | grep ".fasta"`; do `perl /mnt/project/pracstrucfunc12/polyphobius/blastget -db $DB -ix $IN $file > output/$file.blast` wait `/mnt/opt/T-Coffee/bin/kalign -f fasta -input output/$file.blast -output output/$file.msa` wait `perl /mnt/project/pracstrucfunc12/polyphobius/jphobius -poly output/$file.msa &> output/$file.phob` wait done
Signal peptides
The SignalP server with version 4.0 was used.
GO terms
To predict GO terms, the online server of GOPET and ProtFun2.0 were used. To check the pfam family, Pfam was used.