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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 SIMPA96
SIMPA96 is a nearest neighbor secondary structure prediction method. It's based on the homologue method described by Levin et al.

Availability in NPS@
This method is available :

• At URL : https://npsa-prabi.ibcp.fr/NPSA/npsa_simpa96.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
No parameter required

NPS@ SIMPA96 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