segProt: Protein Sequence Segmentation

In nanxstats/Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Protein Sequence Segmentation

Description

Protein Sequence Segmentation

Usage

segProt(
  x,
  aa = c("A", "R", "N", "D", "C", "E", "Q", "G", "H", "I", "L", "K", "M", "F", "P", "S",
    "T", "W", "Y", "V"),
  k = 7
)

Arguments

x	A character vector, as the input protein sequence.
aa	A character, the amino acid type. one of 'A', 'R', 'N', 'D', 'C', 'E', 'Q', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V'.
k	A positive integer, specifys the window size (half of the window), default is 7.

Details

This function extracts the segmentations from the protein sequence.

Value

A named list, each component contains one of the segmentations (a character string), names of the list components are the positions of the specified amino acid in the sequence.

Examples

x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]
segProt(x, aa = 'R', k = 5)

nanxstats/Rcpi documentation built on Sept. 24, 2024, 9:36 a.m.