Difference between revisions of "Lab Journal Task 3 Hemo"

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(Created page with " == Signal Peptides == signalP server Version 4.1 Organism: Eukaryote D-cutoff values: default Input may include TM-helices: yes Restrictions: None")
 
 
(5 intermediate revisions by the same user not shown)
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== 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 ==
  +
  +
For running Polyphobius, the [[https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Polyphobius.pl polyphobius.pl]] script was used in conjuntion with the swissprot database (May 7 2013).
  +
  +
Memsat-SVM was run using the web server.
  +
  +
===voltage-gated potassium channel===
  +
  +
The sequence of 1ORQ starts at position 30 of the Uniprot reference sequence Q9YDF8 and the sequence of 1ORS at position 33. However, the PDB file of 1ORQ contains a start annotation at position 18 and 1ORS a start at position 20. Thus, se added 12 to the positions in the pdb files to get the actual position in the reference sequence Q9YDF8.
   
 
== Signal Peptides ==
 
== Signal Peptides ==
Line 5: Line 54:
 
signalP server Version 4.1
 
signalP server Version 4.1
   
Organism: Eukaryote
+
*Organism: Eukaryote
D-cutoff values: default
+
*D-cutoff values: default
Input may include TM-helices: yes
+
*Input may include TM-helices: yes
Restrictions: None
+
*Restrictions: None
  +
  +
== GO Terms ==
  +
  +
Protfun does not work at the moment due to a server migration. Upon request, the administrator told us that the service won't be available in the next time, since it is seldom used and has a low priority for fixing.

Latest revision as of 00:20, 31 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

For running Polyphobius, the [polyphobius.pl] script was used in conjuntion with the swissprot database (May 7 2013).

Memsat-SVM was run using the web server.

voltage-gated potassium channel

The sequence of 1ORQ starts at position 30 of the Uniprot reference sequence Q9YDF8 and the sequence of 1ORS at position 33. However, the PDB file of 1ORQ contains a start annotation at position 18 and 1ORS a start at position 20. Thus, se added 12 to the positions in the pdb files to get the actual position in the reference sequence Q9YDF8.

Signal Peptides

signalP server Version 4.1

  • Organism: Eukaryote
  • D-cutoff values: default
  • Input may include TM-helices: yes
  • Restrictions: None

GO Terms

Protfun does not work at the moment due to a server migration. Upon request, the administrator told us that the service won't be available in the next time, since it is seldom used and has a low priority for fixing.