UCLA MBI — SERp Server: SER Help

Help Topics: Averaging Window BLAST Seq. ID Cutoff BLAST Sequence count weight BLAST Weight BLAST eValue Cutoff Cluster Limit Cluster Sequence Snippet Cluster Sorting Email Address Entropy Cutoff Entropy Weight Gaps Size Graph Size Graphs High Entropy Residues Last Jobs Maximum Mutations Minimum Mutations Mutable Residues Protein or DNA Sequence Queue Status Result Delivery Method Sec. Str. Cutoff Sec. Str. Weight Secondary Structure Prediction Sequence Identifier Sidechain Entropy Target Residues

The weight assigned to the side chain entropy model. The overall score at each position in the provided sequence is composed of three scores: the secondary structure prediction score, the side chain entropy score and the BLAST search score. By default the weight for the entropy model is 0.5, or half of the secondary structure and BLAST search weights. This is because the cluster pattern analysis provides provides additional emphasis on the side entropies in an indirect way. These weight may be adjusted if one wished to give more emphasis on one of the three models described above. To give the side chain entropy model more consideration, increase this weight to 0.75, 1.0 or even 1.5.

Molecular Biology Institure at the University of California, Los Angeles.