rbd.getBindingSeq: Get Binding Sequence from RBDmap Data

Description Usage Arguments

View source: R/rbd.getBindingSeq.R View source: R/pdb_functions2.R

Description

This funtion gets the binding sequence from RBDmap data

This funtion gets the binding sequence from RBDmap data

Usage

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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)

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

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 Sept. 8, 2018, 9:30 p.m.