compose_GSx7cTerm: Compose a FlyCode GSx7cTerm Amino Acid Sequence

In cpanse/NestLink: NestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles

Compose a FlyCode GSx7cTerm Amino Acid Sequence

Description

composes, out of an as input given amino acid distribution, a randomly sampled amino acid sequence. compose_GPGx8cTerm, compose_GSx7cTerm, and compose_GPx10R belong to three groups composing different flycode (peptide) construction. The construction is given in the function name. For example, GPGx8cTerm, composes a flycode having as prefix GPG followed by eight (x8) amino acids followed by a cTerm sequence. The different construction will have different detectability properties as mass range and hydrophobicity values.

Usage

compose_GSx7cTerm(pool = c(rep("A", 18), rep("S", 6), rep("T", 12),
  rep("N", 1), rep("Q", 1), rep("D", 11), rep("E", 11), rep("V", 12),
  rep("L", 2), rep("F", 1), rep("Y", 4), rep("W", 1), rep("G", 8), rep("P",
  12)), cTerm = c("WR", "WLTVR", "WQEGGR", "WQSR", "WLR"))

Arguments

pool	a vector of amino acids.
cTerm	a vector of a sequence suffix.

Value

a amino acid sequence, e.g., GSAPTTVFGWLTVR.

Author(s)

Christian Panse <[e-mail]> 2015

Examples

 sample.size <- 100
 #
 ## Compose a GSXXXXXXX(WR|WLTVR|WQGGER|WQSR|WLR) peptide
 set.seed(2)
 FC.GSx7cTerm <- replicate(sample.size, compose_GSx7cTerm())
 ## Some Sanity Checks
 table(FC.GSx7cTerm)
 stopifnot(length(FC.GSx7cTerm) == 100)
 FC.PATTERN <- "^GS[ASTNQDEFVLYWGP]{7}(WR|WLTVR|WQEGGR|WLR|WQSR)$"
 stopifnot(
   length(FC.GSx7cTerm[grepl(FC.PATTERN, FC.GSx7cTerm)])
     == sample.size)

cpanse/NestLink documentation built on May 16, 2022, 2:33 a.m.