Protein Sequence Coverage

Measure protein sequence coverage as the union of peptide intervals.

Description

Sequence coverage is the union of supplied peptide intervals on a protein.

Sequence coverage is the union of supplied peptide intervals on a protein. Overlap contributes each residue only once.^[1]

Measure protein sequence coverage as the union of peptide intervals.

When to use Protein Sequence Coverage

Use this tool to measure protein sequence coverage as the union of peptide intervals.

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 Protein Sequence Coverage 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 sequenceLength, peptideStarts, peptideEnds using the field table and calculation rules, then run the tool.
Read coveredResidues, coveragePercent. 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
sequenceLength	Sequence length	number	Required
peptideStarts	Peptide starts	list of number	Required
peptideEnds	Peptide ends	list of number	Required

Enter positive safe-integer length and aligned nonempty safe-integer interval lists. Use zero-based half-open coordinates: 0≤start<end≤length. Union individual covered positions and return residue count and percentage.

coverage%=100 size(union of [start_i,end_i))/sequenceLength

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

Output field	Meaning	Value type
coveredResidues	Covered residues	number
coveragePercent	Coverage percent	number

json

{
  "input": {
    "sequenceLength": 10,
    "peptideStarts": [
      0,
      3,
      8
    ],
    "peptideEnds": [
      5,
      7,
      10
    ]
  },
  "output": {
    "coveredResidues": 9,
    "coveragePercent": 90
  }
}

Limitations and assumptions

Peptide identity and mapping are not verified. Very long intervals require enumeration of individual residue positions, so use bounded sequence lengths.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Unique Peptide Tally: Count peptides unique to each protein in the observed evidence graph. For a complementary task, use Low Complexity Region Fraction: Union long low-complexity stretches and calculate their protein coverage.

References

Protein Sequence Coverage — tool.io

Similar or alternative tools

Unique Peptide Tally
Count peptides unique to each protein in the observed evidence graph.
Low Complexity Region Fraction
Union long low-complexity stretches and calculate their protein coverage.