Find Sequence Motifs.

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

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.

References

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

Author

Barry Grant

See also

regexpr, read.fasta, pdbseq

Examples

# \donttest{
# PDB server connection required - testing excluded

aa.seq <- pdbseq( read.pdb( get.pdb("4q21", URLonly=TRUE) ) )
motif = c("G....GKS")
motif.find(motif, aa.seq)
#> [1] 10 11 12 13 14 15 16 17
# }