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>

For the PsiPred predictions we used the PsiPred Webserver 3.0 with default settings (Mask low complexity regions on).

DSSP predictions were made with DSSP Webserver. PDB files used:

• Q30201 -> 1A6Z
• P10775 -> 2BNH
• Q9X0E6 -> 1KR4
• Q08209 -> 1AUI

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).

GO Terms

For the GO term predictions the webservers were used:

• GOPET
• ProtFun 2.2