Difference between revisions of "Sequence-based predictions Protocol TSD"
m (→Secondary Structure) |
(→Secondary Structure) |
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wget http://www.uniprot.org/uniprot/Q08209.fasta |
wget http://www.uniprot.org/uniprot/Q08209.fasta |
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wget http://www.uniprot.org/uniprot/P06865.fasta |
wget http://www.uniprot.org/uniprot/P06865.fasta |
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| − | </source> |
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| − | |||
| − | Start the predictions |
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| − | <source lang="bash"> |
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| − | #!/bin/bash |
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| − | |||
| − | cd ../input/ |
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| − | |||
| − | for file in `ls | grep .fasta` ; do |
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| − | reprof -i $file -o ../prediction/ |
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| − | done |
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</source> |
</source> |
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| Line 43: | Line 32: | ||
wget http://www.pdb.org/pdb/files/1AUI.pdb |
wget http://www.pdb.org/pdb/files/1AUI.pdb |
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wget http://www.pdb.org/pdb/files/2GJX.pdb |
wget http://www.pdb.org/pdb/files/2GJX.pdb |
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| + | </source> |
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| + | |||
| + | Start the predictions |
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| + | <source lang="bash"> |
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| + | #!/bin/bash |
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| + | |||
| + | cd ../input/ |
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| + | |||
| + | for file in `ls | grep .fasta` ; do |
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| + | reprof -i $file -o ../prediction/ |
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| + | done |
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| + | |||
| + | for file in `ls | grep .pdb` ; do |
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| + | ./../bin/dssp-2.0.4-linux-amd64 -i $file -o ../prediction/$file.dssp |
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| + | done |
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</source> |
</source> |
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Revision as of 16:41, 15 May 2012
Secondary Structure
Get the sequences <source lang="bash">
- !/bin/bash
cd ../input
wget http://www.uniprot.org/uniprot/P10775.fasta wget http://www.uniprot.org/uniprot/Q9X0E6.fasta wget http://www.uniprot.org/uniprot/Q08209.fasta wget http://www.uniprot.org/uniprot/P06865.fasta </source>
For PSIPred use the webserver
For first get the executable <source lang="bash"> wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 chmod +x dssp-2.0.4-linux-amd64 </source>
Get the PDB files for the according Uniprot entries <source lang="bash">
- !/bin/bash
cd ../input
wget http://www.pdb.org/pdb/files/2BNH.pdb wget http://www.pdb.org/pdb/files/1KR4.pdb wget http://www.pdb.org/pdb/files/1AUI.pdb wget http://www.pdb.org/pdb/files/2GJX.pdb </source>
Start the predictions <source lang="bash">
- !/bin/bash
cd ../input/
for file in `ls | grep .fasta` ; do
reprof -i $file -o ../prediction/
done
for file in `ls | grep .pdb` ; do
./../bin/dssp-2.0.4-linux-amd64 -i $file -o ../prediction/$file.dssp
done </source>
Disorder
Get the required sequences <source lang="bash">
- !/bin/bash
cd ../input
wget http://www.uniprot.org/uniprot/P10775.fasta wget http://www.uniprot.org/uniprot/Q9X0E6.fasta wget http://www.uniprot.org/uniprot/Q08209.fasta wget http://www.uniprot.org/uniprot/P06865.fasta </source>
Start the predictions <source lang="bash">
- !/bin/bash
cd /opt/iupred/ END=.iupred
for file in `ls /mnt/home/student/reeb/3_SeqBasedPred/2_DISO/input | grep .fasta` ; do
IFS="."
array=($file)
unset IFS
./iupred /mnt/home/student/reeb/3_SeqBasedPred/2_DISO/input/$file long > /mnt/home/student/reeb/3_SeqBasedPred/2_DISO/predictions/${array[0]}$END
done
</source>
Transmembrane helices
Get the required sequence and our reference sequence <source lang="bash"> cd ../input/
wget http://www.uniprot.org/uniprot/P35462.fasta wget http://www.uniprot.org/uniprot/Q9YDF8.fasta wget http://www.uniprot.org/uniprot/P47863.fasta wget http://www.uniprot.org/uniprot/P06865.fasta </source>
Script for running polyphobius and creating everything needed in advance <source lang="bash">
- !/bin/bash
- $ -S /bin/sh
BLASTDB=$1 #/mnt/project/pracstrucfunc12/data/swissprot/uniprot_sprot
BLASTINDEX=$2 #/mnt/project/pracstrucfunc12/data/index_pp/uniprot_sprot.idx
WD=$3
OUT=$4
EXEC=/mnt/project/pracstrucfunc12/polyphobius/jphobius
EXECBG=/mnt/project/pracstrucfunc12/polyphobius/blastget
EXECKA=/mnt/opt/T-Coffee/bin/kalign
END=.pred
ENDBG=.bg
ENDKA=.msa
PARAMS=-poly
PARAMSKA="-f fasta"
PARAMSBG="-db $BLASTDB -ix $BLASTINDEX"
PATH=$PATH:/mnt/project/pracstrucfunc12/polyphobius/ export PATH
mkdir -p $OUT
cd $WD
pwd
`rm $OUT/log &> /dev/null`
for file in `ls | grep ".fasta"`; do
echo "Processing $file" &>> $OUT/log
IFS="."
array=($file)
unset IFS
`perl $EXECBG $PARAMSBG $file > $OUT/${array[0]}$ENDBG`
wait
if [ `grep "^>" $OUT/${array[0]}$ENDBG | wc -l` -gt 1 ]; then
`$EXECKA $PARAMSKA -input $OUT/${array[0]}$ENDBG -output $OUT/${array[0]}$ENDKA`
wait
`perl $EXEC $PARAMS $OUT/${array[0]}$ENDKA &> $OUT/${array[0]}$END`
wait else
`perl $EXEC $PARAMS $OUT/${array[0]}$ENDBG &> $OUT/${array[0]}$END` fi done </source>
Start the predictions
<source lang="bash"> ./callPolyPhobius.sh /mnt/project/pracstrucfunc12/data/swissprot/uniprot_sprot /mnt/project/pracstrucfunc12/data/index_pp/uniprot_sprot.idx ../input/ ../prediction/sp/ </source>
Signal peptides
<source lang="bash">
- !/bin/bash
for file in /mnt/home/student/reeb/3_SeqBasedPred/4_SIGP/input/*fasta; do
prot=${file##*/}
protein=${prot%.*}
signalp -t euk -graphics gif -d /mnt/home/student/reeb/3_SeqBasedPred/4_SIGP/prediction_v3/gif_$protein -trunc 70 $file > /mnt/home/student/reeb/3_SeqBasedPred/4_SIGP/prediction_v3/$protein.out
done
</source>
GO terms
Start the predictions for the methods by going to their webservers. For GOPet the most recent model, program version and database were used. We also incresed the maximum number of reported GO-Terms to the maxmimum of 100.
