Manual of the CCTOP server
Input formats, prediction types
Sequences can be submitted either with one letter amino acid format as plain text or in FASTA format.
Signal peptide prediction can be turned on, in this case cleavable parts will be removed. It's recommended to have this box checked.
If TMFilter is turned on, the submitted sequence will be checked for membrane spanning regions as an initial step. Unless certain knowledge about the type of the protein is available, it's recommended to check this box, otherwise the HMM architecture behind CCTOP will classify the sequence more likely as a TM protein.
After the submission, it takes around 3-30 minutes to calculate the result, depending on sequence length and server load. When it is finished and an optional email address is provided a notification e-mail will be send to the given address with a link to the page containing the result.