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

• Home
• Teaching
• Publications
• Links
• Contact

If you use this service, could you please send us a mail to npsang@ibcp.fr with details about your usage of the NPSA service (tools used, frequency, type of sequence, ..) ? Could you explain what makes this service unique for you ? Could you please add information about your country and your laboratory ? Thanks

A brief introduction to PREDATOR
PREDATOR is a secondary structure prediction method based on recognition of potentially hydrogen-bonded residues in a single amino acid sequence (original server).

Availability in NPS@
This method is available :

• At URL : https://npsa-prabi.ibcp.fr/NPSA/npsa_predator.html.
• In secondary consensus prediction 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 user can choose between two database files stride.dat and dssp.dat. These files contain propensity tables, secondary structural assignments and thresholds for two secondary structure assignment methods from tertiary structure : STRIDE and DSSP.

NPS@ PREDATOR 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 and below the corresponding predicted states).
• The sequence length.
• The percentage of each secondary element.
• Two graphics. The first to better visualize the prediction. In the second, there are the reliability scores for each predicted state.
• The paramaters used.
• Link on the prediction result text file.

References