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 used in the evolutionary conservation analysis. This analysis locates conserved residues and residues that in other homologs exist are already changed to a target residue. Conserved residues provide a negative contribution to the overall score and hence are disfavored as site for mutation. Residues that in other homologs already exist as one of the target residues have a positive contribution and are hence preferred for mutation. 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 BLAST search is 1 and equivalent to the secondary structure prediction model weight, while the side entropy weight is 0.5 (since the cluster pattern search provides additional emphasis for the side entropies). These weight may be adjusted if one wished to give more emphasis on one of the three models described above.

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