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.

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.

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.