getEnzymeCuts: Add sites of enzymatic cuts (by trypsin, pepsin, and...

In msuprun/bbeaR: an R package and framework for epitope-specific antibody profiling

Usage

getEnzymeCuts(sequence,topo = FALSE, topodb = NULL, rmsignal=T, signalend=24)

Arguments

sequence	amino acid sequence
topo	boolean for a dataframe generated with getTopologyPlotDB()
topodb	name of the getTopologyPlotDB() dataframe
rmsignal	boolean for the removal of the signal peptide chain
signalend	final amino acid residue of the signal chain

Value

The functions returns a data.frame with amino acid positiob (AA.Number) and indicator variables if that position could be enzymatically cut by Pepsin (P), Trypsin (T), or Chymotrypsin (Ch). "Enzyme" column is a cancatenation of P,T,and Ch columns.

Author(s)

Maria Suprun, Randall J. Ellis, Mayte Suárez-Fariñas

Examples

aa.seq<-"MAMAGVFVLFSFVLCGFLPDAAFGAEVDCSRFPNA
TDKEGKDVLVCNKDLRPICGTDGVTYTNDCLLCAYSIEFGTNIS
KEHDGECKETVPMNCSSYANTTSEDGKVMVLCNRAFNPVCGTDG
VTYDNECLLCAHKVEQGASVDKRHDGGCRKELAAVSVDCSEYPK
PDCTAEDRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC"
getEnzymeCuts(aa.seq, topo = FALSE, 
rmsignal = TRUE, signalend = 24)

msuprun/bbeaR documentation built on Jan. 31, 2021, 6:49 p.m.