Task3 Hemochromatosis Protocol

Data Acquisition

Retrieve all sequences: <source lang="bash">

1. !/bin/bash

1. Secondary Structure

cd /mnt/home/student/bernhoferm/mstrprkt/task3/ss/fasta/

wget http://www.uniprot.org/uniprot/Q30201.fasta wget http://www.uniprot.org/uniprot/P10775.fasta wget http://www.uniprot.org/uniprot/Q9X0E6.fasta wget http://www.uniprot.org/uniprot/Q08209.fasta

1. Disorder

cd /mnt/home/student/bernhoferm/mstrprkt/task3/disorder/fasta/

wget http://www.uniprot.org/uniprot/Q30201.fasta wget http://www.uniprot.org/uniprot/P10775.fasta wget http://www.uniprot.org/uniprot/Q9X0E6.fasta wget http://www.uniprot.org/uniprot/Q08209.fasta

1. Transmembrane Helices

cd /mnt/home/student/bernhoferm/mstrprkt/task3/tmh/fasta/

wget http://www.uniprot.org/uniprot/Q30201.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

1. Signal Peptides

cd /mnt/home/student/bernhoferm/mstrprkt/task3/sp/fasta/

wget http://www.uniprot.org/uniprot/Q30201.fasta wget http://www.uniprot.org/uniprot/P02768.fasta wget http://www.uniprot.org/uniprot/P47863.fasta wget http://www.uniprot.org/uniprot/P11279.fasta </source>

Secondary Structure

ReProf predictions: <source lang="bash">

1. !/bin/bash

1. Secondary Structure

cd /mnt/home/student/bernhoferm/mstrprkt/task3/ss/fasta/

reprof -i Q30201.fasta -o ../pred/ &> ../Q30201.log reprof -i P10775.fasta -o ../pred/ &> ../P10775.log reprof -i Q9X0E6.fasta -o ../pred/ &> ../Q9X0E6.log reprof -i Q08209.fasta -o ../pred/ &> ../Q08209.log </source>

Disorder

IUPred predictions: <source lang="bash">

1. !/bin/bash

1. Disorder

DIS="/mnt/home/student/bernhoferm/mstrprkt/task3/disorder" cd /opt/iupred/

iupred $DIS/fasta/Q30201.fasta long > $DIS/pred/Q30201.pred iupred $DIS/fasta/P10775.fasta long > $DIS/pred/P10775.pred iupred $DIS/fasta/Q9X0E6.fasta long > $DIS/pred/Q9X0E6.pred iupred $DIS/fasta/Q08209.fasta long > $DIS/pred/Q08209.pred </source>

Transmembrane Helices

PolyPhobius preprocessing: <source lang="bash">

1. !/bin/bash

1. Transmembrane Helices

TMH="/mnt/home/student/bernhoferm/mstrprkt/task3/tmh" BG="/mnt/project/pracstrucfunc12/polyphobius/blastget" DB="/mnt/project/pracstrucfunc12/data/swissprot/uniprot_sprot" DBI="/mnt/project/pracstrucfunc12/data/index_pp/uniprot_sprot.idx" KAL="/mnt/opt/T-Coffee/bin/kalign"

`perl $BG -db $DB -ix $DBI $TMH/fasta/Q30201.fasta > $TMH/tmp/Q30201.bgout` $KAL -f fasta -input $TMH/tmp/Q30201.bgout -output $TMH/tmp/Q30201.kalout

`perl $BG -db $DB -ix $DBI $TMH/fasta/P35462.fasta > $TMH/tmp/P35462.bgout` $KAL -f fasta -input $TMH/tmp/P35462.bgout -output $TMH/tmp/P35462.kalout

`perl $BG -db $DB -ix $DBI $TMH/fasta/Q9YDF8.fasta > $TMH/tmp/Q9YDF8.bgout` $KAL -f fasta -input $TMH/tmp/Q9YDF8.bgout -output $TMH/tmp/Q9YDF8.kalout

`perl $BG -db $DB -ix $DBI $TMH/fasta/P47863.fasta > $TMH/tmp/P47863.bgout` $KAL -f fasta -input $TMH/tmp/P47863.bgout -output $TMH/tmp/P47863.kalout </source>

PolyPhobius predictions: <source lang="bash">

1. !/bin/bash

1. Transmembrane Helices

TMH="/mnt/home/student/bernhoferm/mstrprkt/task3/tmh" POL="/mnt/project/pracstrucfunc12/polyphobius/jphobius"

PATH=$PATH:/mnt/project/pracstrucfunc12/polyphobius/ export PATH

$POL -poly $TMH/tmp/Q30201.kalout > $TMH/pred/Q30201.pol $POL -poly $TMH/tmp/P35462.kalout > $TMH/pred/P35462.pol $POL -poly $TMH/tmp/Q9YDF8.kalout > $TMH/pred/Q9YDF8.pol $POL -poly $TMH/tmp/P47863.kalout > $TMH/pred/P47863.pol </source>

Signal Peptides

We used the SignalP Webserver 4.0 for the predictions. Settings were not changed (i.e. we used the default settings).