Difference between revisions of "Lab Journal Task 3 Hemo"
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== Secondary Structure Predictions == |
== Secondary Structure Predictions == |
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+ | * reprof version 1.0.1 |
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− | === Output unification == |
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+ | * psipred version 3.3 |
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+ | |||
+ | The PSSMs used for reprof were selected from the psiblast runs against big_80, SwissProt and PDB with standard parameters (2 iterations and e-value cutoff of 0.002) that were already performed in task2. |
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+ | Reprof was called using |
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+ | reprof -i <input file> |
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+ | |||
+ | The Psipred server was run only using the sequences and not with a multiple sequence alignment. |
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+ | |||
+ | === Output unification === |
||
DSSP, reprof and psipred all have different output types. In order to compare the results, the following mappings were performed |
DSSP, reprof and psipred all have different output types. In order to compare the results, the following mappings were performed |
||
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== Disorder Prediction == |
== Disorder Prediction == |
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+ | |||
+ | The IUPred server was used to generate the corresponding predictions. But unfortunately, the server does not show a version number. |
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+ | |||
+ | Metadisorder was called using the predictprotein command specified in the task description. |
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== Transmembrane Helix Prediction == |
== Transmembrane Helix Prediction == |
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+ | === Polyphobius === |
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+ | For running polyphobius, the [[https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Polyphobius.pl polyphobius.pl]] script was used in conjuntion with t |
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Revision as of 16:16, 30 August 2013
Contents
Secondary Structure Predictions
- reprof version 1.0.1
- psipred version 3.3
The PSSMs used for reprof were selected from the psiblast runs against big_80, SwissProt and PDB with standard parameters (2 iterations and e-value cutoff of 0.002) that were already performed in task2. Reprof was called using
reprof -i <input file>
The Psipred server was run only using the sequences and not with a multiple sequence alignment.
Output unification
DSSP, reprof and psipred all have different output types. In order to compare the results, the following mappings were performed
- reprof
- H helix
- E extended
- L loop -> C
- DSSP
- H = alpha helix -> H
- B = residue in isolated beta-bridge -> C
- E = extended strand, participates in beta ladder -> E
- G = 3-helix (3/10 helix) -> H
- I = 5 helix (pi helix) -> C
- T = hydrogen bonded turn - C
- S = bend -> C
psipred:
- H helix
- E sheet
- C disordered
Disorder Prediction
The IUPred server was used to generate the corresponding predictions. But unfortunately, the server does not show a version number.
Metadisorder was called using the predictprotein command specified in the task description.
Transmembrane Helix Prediction
Polyphobius
For running polyphobius, the [polyphobius.pl] script was used in conjuntion with t
Signal Peptides
signalP server Version 4.1
- Organism: Eukaryote
- D-cutoff values: default
- Input may include TM-helices: yes
- Restrictions: None