regex.search: Searching for motifs using regular expressions (REGEX)

In effectR: Predicts Oomycete Effectors

Description

This function uses searches a list of SeqFastadna objects for sequences with RxLR or CRN motifs.

Usage

regex.search(sequence, motif = "RxLR", reg.pat = NULL)

Arguments

sequence	A list of SeqFastadna objects from seqinr read.fasta. The SeqFastadna object must be comprised by amino acid sequences, not DNA sequences
motif	A character string indicating the motif to be searched. Motifs for two cytoplasmic effectors are added to the function: RxLR or CRN effectors. Each of these motifs are associated with a by-default REGEX (reg.pat).These motifs are adapted from Haas et al. (2009). A third option, custom, allows for the search of custom motifs. The custom option requires the specification of the motif REGEX pattern in the reg.pat option, in a regex format. Default motif is RxLR
reg.pat	A character string indicating the REGEX pattern for the custom motif. The specification of the REGEX pattern in must be in regex format. Required for custom option of motif

References

Haas, B.J., Kamoun, S., Zody, M.C., Jiang, R.H., Handsaker, R.E., Cano, L.M., Grabherr, M., Kodira, C.D., Raffaele, S., Torto-Alalibo, T. and Bozkurt, T.O., 2009. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature, 461(7262), p.393.

Examples

fasta.file <- system.file("extdata", "test_infestans.fasta", package = "effectR")
ORF <- seqinr::read.fasta(fasta.file)
rxlr.cand <- regex.search(ORF)
custom.cand <- regex.search(ORF, motif = "custom", reg.pat ="^\\w{12,60}r\\wlr\\w{6,10}eer")

effectR documentation built on May 1, 2019, 7:28 p.m.