Sequence-based predictions Protocol TSD

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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">

1. !/bin/bash
2. $ -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>