Difference between revisions of "Lab Journal Task 3 Hemo"

From Bioinformatikpedia
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== Secondary Structure Predictions ==
 
== Secondary Structure Predictions ==
   
  +
* reprof version 1.0.1
=== Output unification ==
 
  +
* 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
 
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 ==
  +
  +
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 ==
 
== Transmembrane Helix Prediction ==
   
  +
=== Polyphobius ===
  +
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
   
   

Revision as of 17:16, 30 August 2013

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

GO Terms