rbd.getBindingSeq: Get Binding Sequence from RBDmap Data - Zhang et. al 2019...

In egmg726/crisscrosslinker: An R package for protein interaction analysis

Description

This function gets the binding sequence from RBDmap data

Usage

rbd.getBindingSeq(
  ms_sequence,
  protease,
  sequence_for_alignment,
  protein_name = NULL,
  database_name = NULL,
  database_id = NULL,
  cleave_offset = 0,
  last_aa = NULL,
  include_ambiguous = FALSE,
  proteolytic_fragments = FALSE
)

Arguments

ms_sequence	The input sequence from MS, should be loaded as a string
protease	The protease used for the experiment, either 'ArgC' or 'LysC'
sequence_for_alignment	The sequence to find the binding sequence in. The ms_sequence must be within the sequence_for_alignment or NULL will be returned.
protein_name	Name of the protein to which the sequence_for_alignment belongs. Defaults to NULL
database_name	Name of the database used: 'PDB','UniProt' or 'FASTA' (for the input FASTA sequence). Defaults to NULL
database_id	Identifier for the database. Defaults to NULL
cleave_offset	Cleave offset for the sequence. Defaults to 0

egmg726/crisscrosslinker documentation built on Jan. 23, 2021, 1:50 a.m.