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Using the CASVM server

The CASVM server accepts user input through an intuitive web form:

Submitting your sequence:

  1. Enter ONE protein sequence in the input box. Sequence must be raw or FASTA format. Raw formatted sequences have the FASTA header removed.
  2. Sequence should be greater than 25 amino acids in length. Ensure that there are no non-standard amino acids in your sequence.
  3. Enter a name for your submitted sequence (optional).
  4. Select the scanning window size. Your sequence will be scanned from N-terminal to the C-terminal with a sliding window of the specified length. When a potential P1 residue is encountered , sequence segments (of length equal to the selected scanning window) flanking the P1 residue will be extracted for SVM prediction. The type of SVM classifier used for prediction will be selected based on the scanning window size. For example, if the P4P2' scanning window is selected, the P4P2'-trained SVM classifier will be used for prediction. Due to the window size, not all amino acids in the submitted sequence will be used for prediction. If the P14P10' window is selected, the first and last ten residues of the sequence will be ignored. The P14P10' window is selected as default as it was shown to be have the highest accuracy.
  5. Select the type of P1 residue. If aspartic acid is selected, only sequence segments of the scanning window size containing aspartic acid at the P1 position will be extracted for SVM prediction. Default selection is aspartic acid.
  6. Click the "Cleave it!" button to submit your sequence for prediction.

Interpreting the server results:

Server results are presented in a table format containing:

  1. Name of submitted protein,
  2. An abbreviated version of the submiited sequence (only first and last 5 amino acids are shown)
  3. Length of sequence
  4. Potential caspase cleavage sites. A list containing all tetrapeptide subsequences within the submitted sequence containing the specified P1 residue. For example, if aspartic acid was selected during submission, all tetrapeptide subsequences with aspartic acid at P1 wil be shown as potential caspase cleavage sites. Number to the right of the tetrapeptides indicate the position of the P1 residue in the submitted sequence.
  5. Predicted sites. A list displaying the tetrapeptide subsequences which were predicted to be cleavage sites by the SVM algorithm. Number to the right of the tetrapeptides indicate the position of the P1 residue in the submitted sequence.