A brief introduction to SOPMA
SOPMA (Self-Optimized Prediction Method with Alignment) is an improvement of SOPM method. These methods are based on the homologue method of Levin et al.. The improvent takes place in the fact that SOPMA takes into account information from an alignment of sequences belonging to the same family. If there are no homologous sequences the SOPMA prediction is the SOPM one.
Warning : It can take up to 5 minutes to compute SOPMA for a sequence (45 seconds for RBTR_KLEAE (270 aa) and 4'33 minutes for MDR3_HUMAN (1270 aa) ). So, be careful when using it in alignment (the total computing time can't be above 2 hours on NPS@).
NPS@ is the orginal server for this method.
Availability in NPS@
This method is available :
You can set the number of conformational states to predict : 3 or 4.
The similarity threshold parameter is the threshold below which a subject peptide is rejected when it's compared with a query peptide of the sequence.
The window size parameter sets the length of the peptides to use.
NPS@ SOPMA output example
You can see: