Lab Journal Task 3 Hemo
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.
DSSP, reprof and psipred all have different output types. In order to compare the results, the following mappings were performed
- H helix
- E extended
- L loop -> C
- 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
- H helix
- E sheet
- C disordered
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.
signalP server Version 4.1
- Organism: Eukaryote
- D-cutoff values: default
- Input may include TM-helices: yes
- Restrictions: None
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.