• PRABI-GERLAND
  RHONE-ALPES BIOINFORMATIC POLE GERLAND SITE
• Institute of Biology and Protein Chemistry

• Home
• Teaching
• Publications
• Links
• Contact

The secondary structure consensus prediction
Combining methods using differents approaches to predict secondary structure is useful to validate the prediction. The first step is to select the secondary structure prediction methods (see below) you want to use. Then, the secondary structure consensus prediction program generates a secondary consensus. In this consensus the most present predicted conformational state is reported for each residue.
Secondary structure prediction methods available are :

• DPM
• DSC
• GORI
• GORIII
• GORIV
• HNN
• MLRC
• PHD
• PREDATOR
• SIMPA96
• SOPM
• SOPMA

Availability in NPS@
This method is available :

• At URL : https://npsa-prabi.ibcp.fr/NPSA/npsa_seccons.html.
• In protein sequences multiple alignement at URLs :
  • CLUSTALW : https://npsa-prabi.ibcp.fr/NPSA/npsa_clustalw.html
  • MULTALIN : https://npsa-prabi.ibcp.fr/NPSA/npsa_multalin.html
• when you work with a sequence in NPS@ if you make a consensus secondary prediction on it.

Parameters
The paramaters available are those of the individual methods above.

NPS@ Secondary consensus output example
You can see:

• MPSA/ANTHEPROT link to view the prediction in these local protein sequence analysis softwares.
• The color coded prediction. A sequence line is followed by each individual prediction and by the secondary consensus (Sec.Cons line).
• The sequence length.
• The percentage of each secondary element for each prediction method.
• A graphic to better visualize the prediction.
• The paramaters used.
• Links on the indvidual prediction result file to see them in MPSA/ANTHEPROT.

References