Difference between revisions of "Task3 Hemochromatosis Protocol"
Bernhoferm (talk | contribs) |
Bernhoferm (talk | contribs) (→Data Acquisition) |
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wget http://www.uniprot.org/uniprot/P11279.fasta |
wget http://www.uniprot.org/uniprot/P11279.fasta |
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</source> |
</source> |
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=== Secondary Structure === |
=== Secondary Structure === |
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For the PsiPred predictions we used the [http://bioinf.cs.ucl.ac.uk/psipred/ PsiPred Webserver 3.0] with default settings (Mask low complexity regions on). |
For the PsiPred predictions we used the [http://bioinf.cs.ucl.ac.uk/psipred/ PsiPred Webserver 3.0] with default settings (Mask low complexity regions on). |
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=== Disorder === |
=== Disorder === |
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iupred $DIS/fasta/Q08209.fasta long > $DIS/pred/Q08209.pred |
iupred $DIS/fasta/Q08209.fasta long > $DIS/pred/Q08209.pred |
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</source> |
</source> |
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=== Transmembrane Helices === |
=== Transmembrane Helices === |
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$POL -poly $TMH/tmp/P47863.kalout > $TMH/pred/P47863.pol |
$POL -poly $TMH/tmp/P47863.kalout > $TMH/pred/P47863.pol |
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</source> |
</source> |
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=== Signal Peptides === |
=== Signal Peptides === |
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We used the [http://www.cbs.dtu.dk/services/SignalP/ SignalP Webserver 4.0] for the predictions. |
We used the [http://www.cbs.dtu.dk/services/SignalP/ SignalP Webserver 4.0] for the predictions. |
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Settings were not changed (i.e. we used the default settings). |
Settings were not changed (i.e. we used the default settings). |
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=== GO Terms === |
=== GO Terms === |
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* [http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.startthis?SIMGO=w2h.welcome GOPET] |
* [http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.startthis?SIMGO=w2h.welcome GOPET] |
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* [http://www.cbs.dtu.dk/services/ProtFun/ ProtFun 2.2] |
* [http://www.cbs.dtu.dk/services/ProtFun/ ProtFun 2.2] |
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== Other Scripts == |
== Other Scripts == |
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Revision as of 12:52, 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>
For the PsiPred predictions we used the PsiPred Webserver 3.0 with default settings (Mask low complexity regions on).
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>
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:
