Protease Digest

Simulate sequence digestion from caller-specified cut and blocking residues.

Description

A configurable protease digest splits after caller-selected residues unless a selected blocking residue follows.

A configurable protease digest splits after caller-selected residues unless a selected blocking residue follows. The rule is explicitly supplied rather than inferred from an enzyme name.^[1]

Simulate sequence digestion from caller-specified cut and blocking residues.

When to use Protease Digest

Use this tool to simulate sequence digestion from caller-specified cut and blocking residues.

Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.

How to use Protease Digest and understand its results

Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
Enter sequence, cleaveAfter, blockedNext using the field table and calculation rules, then run the tool.
Read digestedPeptides, cleavagePositions. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
sequence	Sequence	string	Required
cleaveAfter	Cleave after	string	Required
blockedNext	Blocked next	string	Required

Enter a canonical sequence and case-sensitive residue-set strings. Check internal boundaries, split at exclusive cut positions and return ordered peptides and cuts. Empty sets are allowed; no internal cut is created after the terminal residue.

The shared sequence helper trims outer whitespace and uppercases the sequence. It requires at least one residue from ACDEFGHIKLMNPQRSTVWY. Internal whitespace, FASTA headers, ambiguous letters and modified-residue notation are rejected. Sequence indexes refer to the normalized sequence; individual tools may preserve original strings in their returned lists as explained above.

cut after residue in cleaveAfter when next residue is absent from blockedNext

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
digestedPeptides	Digested peptides	list of string
cleavagePositions	Cleavage positions	list of number

json

{
  "input": {
    "sequence": "AKPAKR",
    "cleaveAfter": "KR",
    "blockedNext": "P"
  },
  "output": {
    "digestedPeptides": [
      "AKPAK",
      "R"
    ],
    "cleavagePositions": [
      5
    ]
  }
}

Limitations and assumptions

Only the sequence is normalized. Lowercase cut/block strings do not match uppercase residues. No missed-cleavage, enzyme kinetics or modification effect is modeled.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Tryptic Peptides: Generate fully tryptic peptides with K/R cleavage blocked before proline. For a complementary task, use GLUC Cleavage: Locate Glu-C acidic-residue cleavage sites with a caller Asp option.

References

Protease Digest — tool.io

Similar or alternative tools

Tryptic Peptides
Generate fully tryptic peptides with K/R cleavage blocked before proline.
GLUC Cleavage
Locate Glu-C acidic-residue cleavage sites with a caller Asp option.