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

Five different graphs can be generated to aid visualization of the results: The Score Summary graph attempts to summarize all results. It is a stacked graph that shows the combined score for each residue in the sequence, and the factors making up the score. In addition, residues proposed for mutation in each cluster, and the pattern of high entropy and low entropy amino acids prior and after the introduction of the proposed mutation are shown. The BLAST Conservation graph shows the number of sequences that either have the original residue (conservation) or one of the target residues in the aligned sequence. Regions with high conservation can be easily identified. The Entropy Average graph shows the averaged side chain entropy profile for the sequence. Regions with high entropy (peaks) can be easily identified. The Secondary Structure graph shown the PSIPRED prediction results. Regions predicted to be in Helices, Strands or Coils are easily identified. The Coil Secondary Structure graph is same as the complete secondary structure prediction graph, except it only shows the prediction for coil regions, which is used for further analysis.

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