Difference between revisions of "Task3 Hemochromatosis Protocol"
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=== Transmembrane Helices === |
=== Transmembrane Helices === |
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| + | |||
| + | PolyPhobius preprocessing: |
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| + | <source lang="bash"> |
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| + | #!/bin/bash |
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| + | |||
| + | #Transmembrane Helices |
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| + | TMH="/mnt/home/student/bernhoferm/mstrprkt/task3/tmh" |
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| + | BG="/mnt/project/pracstrucfunc12/polyphobius/blastget" |
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| + | DB="/mnt/project/pracstrucfunc12/data/swissprot/uniprot_sprot" |
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| + | DBI="/mnt/project/pracstrucfunc12/data/index_pp/uniprot_sprot.idx" |
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| + | KAL="/mnt/opt/T-Coffee/bin/kalign" |
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| + | |||
| + | |||
| + | `perl $BG -db $DB -ix $DBI $TMH/fasta/Q30201.fasta > $TMH/tmp/Q30201.bgout` |
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| + | $KAL -f fasta -input $TMH/tmp/Q30201.bgout -output $TMH/tmp/Q30201.kalout |
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| + | |||
| + | `perl $BG -db $DB -ix $DBI $TMH/fasta/P35462.fasta > $TMH/tmp/P35462.bgout` |
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| + | $KAL -f fasta -input $TMH/tmp/P35462.bgout -output $TMH/tmp/P35462.kalout |
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| + | |||
| + | `perl $BG -db $DB -ix $DBI $TMH/fasta/Q9YDF8.fasta > $TMH/tmp/Q9YDF8.bgout` |
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| + | $KAL -f fasta -input $TMH/tmp/Q9YDF8.bgout -output $TMH/tmp/Q9YDF8.kalout |
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| + | |||
| + | `perl $BG -db $DB -ix $DBI $TMH/fasta/P47863.fasta > $TMH/tmp/P47863.bgout` |
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| + | $KAL -f fasta -input $TMH/tmp/P47863.bgout -output $TMH/tmp/P47863.kalout |
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| + | </source> |
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| + | |||
| + | PolyPhobius predictions: |
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| + | <source lang="bash"> |
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| + | #!/bin/bash |
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| + | |||
| + | #Transmembrane Helices |
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| + | TMH="/mnt/home/student/bernhoferm/mstrprkt/task3/tmh" |
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| + | POL="/mnt/project/pracstrucfunc12/polyphobius/jphobius" |
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| + | |||
| + | PATH=$PATH:/mnt/project/pracstrucfunc12/polyphobius/ |
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| + | export PATH |
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| + | |||
| + | $POL -poly $TMH/tmp/Q30201.kalout > $TMH/pred/Q30201.pol |
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| + | $POL -poly $TMH/tmp/P35462.kalout > $TMH/pred/P35462.pol |
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| + | $POL -poly $TMH/tmp/Q9YDF8.kalout > $TMH/pred/Q9YDF8.pol |
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| + | $POL -poly $TMH/tmp/P47863.kalout > $TMH/pred/P47863.pol |
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| + | </source> |
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=== Signal Peptides === |
=== Signal Peptides === |
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Revision as of 12:01, 17 May 2012
Contents
Data Acquisition
Retrieve all sequences: <source lang="bash">
- !/bin/bash
- 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
- 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
- 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
- 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">
- !/bin/bash
- 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">
- !/bin/bash
- 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">
- !/bin/bash
- 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 $TMH/tmp/P47863.kalout </source>
PolyPhobius predictions: <source lang="bash">
- !/bin/bash
- Transmembrane Helices
TMH="/mnt/home/student/bernhoferm/mstrprkt/task3/tmh" POL="/mnt/project/pracstrucfunc12/polyphobius/jphobius"
PATH=$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>
