searchSLiMs: searchSLiMs

In BIMSBbioinfo/slimR: Short Linear Motif (SLiM) Analysis in the context of human diseases

Description

Using regular expressions of SLiMs, find all matches of given SLiM patterns in a given sequence

Usage

searchSLiMs(sequence, motifRegex, from = 1, to = nchar(sequence))

Arguments

sequence	Protein sequence using amino acid alphabet
motifRegex	A list object where names of the list are ELM identifiers and each list item has one ELM regex
from	integer value (default: 1) where to start the search for patterns
to	integer value (default: length of input sequence) where to end the search

Value

A vector of motif hits with the syntax: <MotifIdentifier>:<start position in sequence>:<end position in sequence> e.g.: TRG_ENDOCYTIC_2:333:340

Examples

glutFastaFile <- system.file("extdata", "glut.fasta", package = 'slimR')
glutFasta <- Biostrings::readAAStringSet(glutFastaFile)

slims <- searchSLiMs(paste(glutFasta), slimR::motifRegex)

BIMSBbioinfo/slimR documentation built on Nov. 4, 2021, 6:48 a.m.