LYSC Cleavage

Locate Lys-C cleavage sites after internal lysines.

Description

Lys-C cleavage-site enumeration lists internal boundaries after lysines.

Lys-C cleavage-site enumeration lists internal boundaries after lysines. Here proline does not block a lysine cut.^[1]

Locate Lys-C cleavage sites after internal lysines.

When to use LYSC Cleavage

Use this tool to locate Lys-C cleavage sites after internal lysines.

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 LYSC Cleavage 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 using the field table and calculation rules, then run the tool.
Read cleavagePositions, cleavageCount. 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

Enter a canonical sequence. Return ascending exclusive slice boundaries and cut count, omitting the final residue as an internal boundary.

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.

cutPosition=i+1 for each internal K

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

Output field	Meaning	Value type
cleavagePositions	Cleavage positions	list of number
cleavageCount	Cleavage count	number

json

{
  "input": {
    "sequence": "AKAKKA"
  },
  "output": {
    "cleavagePositions": [
      2,
      4,
      5
    ],
    "cleavageCount": 3
  }
}

Limitations and assumptions

This is a simplified site rule rather than a digestion-yield model. Modifications, reaction conditions and missed cleavages are not considered.

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 Trypsin Cleavage Sites: Locate trypsin cut positions at K/R not followed by proline. For a complementary task, use Protease Digest: Simulate sequence digestion from caller-specified cut and blocking residues.

References

LYSC Cleavage — tool.io

Similar or alternative tools

Trypsin Cleavage Sites
Locate trypsin cut positions at K/R not followed by proline.
Protease Digest
Simulate sequence digestion from caller-specified cut and blocking residues.