Difference between revisions of "Sequence-based predictions Protocol TSD"
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== Transmembrane helices == |
== Transmembrane helices == |
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Get the required sequence and our reference sequence |
Get the required sequence and our reference sequence |
Revision as of 22:46, 8 May 2012
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>