compose_GPx10R: Compose a peptide with a defined AA 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 peptide with a defined AA 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_GPx10R(aa_pool1, aa_pool2)

Arguments

aa_pool1	AA distributen.
aa_pool2	AA distributen.

Value

a AA sequence

Author(s)

Christian Panse <[e-mail]> 2015

Examples

set.seed(1)
aa_pool_1_2_9_10 <- c(rep('A', 8), rep('S', 7), rep('T', 7), rep('N', 6),
rep('Q', 6), rep('D', 8), rep('E', 8), rep('V', 9), rep('L', 6), rep('F', 5),
rep('Y', 9), rep('W', 6), rep('G', 15), rep('P', 0))

aa_pool_3_8 <- c(rep('A', 5), rep('S', 4), rep('T', 5), rep('N', 2),
rep('Q', 2), rep('D', 8), rep('E', 8), rep('V', 7), rep('L', 5), rep('F', 4),
rep('Y', 6), rep('W', 4), rep('G', 12), rep('P', 28))

compose_GPx10R(aa_pool_1_2_9_10, aa_pool_3_8)
(FlyCodes <- replicate(10, compose_GPx10R(aa_pool_1_2_9_10, aa_pool_3_8)))
plot(parentIonMass(FlyCodes) ~ssrc(FlyCodes))

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