Annotate cleavage-site efficiency

annotate_cleavage_sites() classifies sequence-local cleavage-site efficiency for trypsin-family digests. Companion to digest_protein() for inspecting cleavage hotspots before or alongside peptide generation.

Usage

annotate_cleavage_sites(sequence, enzyme = "trypsin")

Arguments

sequence

Protein input supplied as a single sequence, a named character vector of length 1, a Biostrings::AAString, or a FASTA file path resolving to exactly one protein. NULL, length-zero, and wrong-type inputs raise pepvet_error_invalid_input; NA and empty strings raise pepvet_error_invalid_sequence. Malformed FASTA files raise a classed pepvet_error_invalid_input error.

enzyme

Cleavage rule name. Defaults to "trypsin". Cleavage-efficiency annotations are implemented for the trypsin family only: trypsin, trypsin-high, trypsin-low, and trypsin-simple. Supported non-trypsin names raise pepvet_error_unsupported_cleavage_annotation; missing, empty, wrong-type, and unrecognized values raise pepvet_error_invalid_enzyme.

Value

A tibble with one row per candidate cleavage site and the columns position, residue, flanking_context, efficiency, and rule_applied. Returns an empty tibble when the sequence contains no trypsin cleavage sites.

Details

The current annotations are sequence-local and based on P1-P1' context only. They do not model higher-order structural accessibility, extended subsite preferences beyond P1', or PTMs that block cleavage. Unsupported enzymes raise an error rather than returning a partially annotated table.

Limitations

Trypsin family only, sequence-local P1-P1' context only, no extended subsite modeling.

See also

Other digest: digest_protein()

Examples

annotate_cleavage_sites("AKRTPK", enzyme = "trypsin")
#> # A tibble: 2 × 5
#>   position residue flanking_context efficiency rule_applied           
#>      <int> <chr>   <chr>            <chr>      <chr>                  
#> 1        2 K       AKRT             medium     adjacent_basic_residues
#> 2        3 R       AKRTP            high       default_trypsin_site