segProt: Protein Sequence Segmentation

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

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.

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

Examples

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

BioMedR documentation built on July 5, 2019, 9:03 a.m.