motif.find: Find Sequence Motifs.

In bio3d: Biological Structure Analysis

Find Sequence Motifs.

Description

Return Position Indices of a Short Sequence Motif Within a Larger Sequence.

Usage

motif.find(motif, sequence)

Arguments

motif	a character vector of the short sequence motif.
sequence	a character vector of the larger sequence.

Details

The sequence and the motif can be given as a either a multiple or single element character vector. The dot character and other valid regexpr characters are allowed in the motif, see examples.

Value

Returns a vector of position indices within the sequence where the motif was found, see examples.

Author(s)

Barry Grant

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

See Also

regexpr, read.fasta, pdbseq

Examples

# PDB server connection required - testing excluded
try({

aa.seq <- pdbseq( read.pdb( get.pdb("4q21", URLonly=TRUE) ) )
motif = c("G....GKS")
motif.find(motif, aa.seq)

}, silent=TRUE)
if(inherits(.Last.value, "try-error")) {
   message("Need internet to run the example")
}

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.