Sequence Name
This is an optional field. It can have any alphabet and numbers with "-" or "_".All other character are non-permissible.E-mail Address
This is an optional field. Depending on the server load and number of sequences and length of each sequence, CBTOPE might take some time to serve the query. User can provide the Email ID to get the result through email however result will be printed on the screen itself after job completion. The page can be bookmarked for later reference.Sequence Input and Format
Amino acid sequences must be entered in the standard FASTA format. Sequence(s) can be pasted or can be given as a file. All the non standard characters like [*&^%$@#!()_+~=;'",<>?.\|} are ignored from the sequence.The warning is displayed if the user submit input from both sources or no sequence is submitted.SVM Threshold and Output
During prediction each amino acid of the sequence gets a SVM score. user need to set the threshold above which amino acid residue would be considered as epitope otherwise non-epitope. By Default it is -0.3 which was observed during the development of server. If you want more confidence or high specificity in the prediction, we recommend setting higher value. Residues will be coloured and underlined if SVM score is greater than selected threshold.Each amino acid is assigned a probability value based on the scale ranging from 0 to 9 (row 3).
Higher the value higher the probability of being that residue as antibody epitope. This scale is independent of Selected Threshold.
Secondary structure state of each residue is predicted using PSIPRED program. Secondary structure state can provide an idea of False positive prediciton as probabibilty of finding Conformational B cell epitopes is more in the Coiled or turn region than in the helix or Beta sheet.