Results of Automatic RMA system                                 BACK

The automatic RMA system extracts unique peptide motifs with a degree value above the default lower limit after performing the strict merging operation. The segments in light blue or dark blue are the unique peptide motifs that fit in with the strict with a length longer than the default limits( 8 for amino acid and 15 for DNA sequences), whereas the segments in purple are the overlapping regions between two unique peptide motifs.


Results of Semi-Automatic RMA system                         BACK

The semi-automatic RMA system provides four different merging methods to enhance different uniqueness levels. The searched results are shown in different colors to distinish their performance, each condition is described in the following section.

Case 1. Merge Operator
The results display the unique peptide motifs with a degree value above the lower limit after performing the merge operation(i.e. only the unique peptide motifs that fit in with the merging criterion with a length longer than the lower limit are shown). The segments in red or dark red are the unique peptide motifs with a length longer than the lower limit, whereas the segments in green or dark green are the unique peptide motifs with a length shorter than the lower limit.

Case 2. Trim Merge Operator
The results display the unique peptide motifs with a degree value above the lower limit after performing the merge operation, and the imperfectly unique residues at the two ends of the peptide motifs are trimmed. The segments in red or dark red are the unique peptide motifs with a length longer than the lower limit, whereas the segments in green or dark green are the unique peptide motifs with a length shorter than the lower limit. The yellow regions represent the trimmed residues.

Case 3. Strict Merge Operator
The results display the unique peptide motifs with a degree value above the lower limit after performing the strict merge operation(i.e. only the unique peptide motifs that fit in with the strict with a length longer than the lower limit are shown). The segments in light blue or dark blue are the unique peptide motifs that fit in with the strict with a length longer than the lower limit, whereas the segments in purple are the overlapping regions between two unique peptide motifs.

Case 4. Strict Trim Merge Operator
The results display the unique peptide motifs with a degree value above the lower limit after performing the strict merge operation, and the imperfectly unique residues at the two ends of the peptide motifs are trimmed. The segments in light blue or dark blue are the unique peptide motifs that fit in with the strict with a length longer than the lower limit, whereas the segments in purple are the overlapping regions between two unique peptide motifs. The yellow regions represent the trimmed residues.

 

Description of the priority for ranking the unique peptide motifs

The unique peptide motifs are ranked according to four characteristics: hydrophilicity and charge of the residues, number of prolines in the motifs, and the proximity of the motifs towards the N- or C-terminal of the protein. The higher position in the rank indicates the better antigenicity of the unique peptide motif; hence the motif may be a suitable epitope for generation of antibodies.

 

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