Is there an R function that can find (like count) and give position of string?

Question

I am looking for code in Rstudio that will search for Recombination signal sequences (RSS) within a DNA sequence and give me the position. I used count function however it does not give me position and I cannot input multiple RSSs into it at the same time which makes it very tedious. For instance:

cd247<-read.fasta("sequence.fasta")
#store DNA sequence for cd247 into cd247seq
cd247seq<-cd247[[1]]
cd247seq[1:50]
#change cd247seq from vector of characters to string
c2s(cd247seq)
#create table of all the 7 character sequences in cd247 gene
count(cd247seq,7)
cd247table<-count(cd247seq,7)
cd247table[["tactgtg"]]

outputs

cd247table[["tactgtg"]]

[1] 1

but not position within cd247seq

I have posted my files to github https://github.com/opheelorraine/Map-RSS

Answer 1

Have a look at the Biostrings package, in particular the matchPDict function. See https://kasperdanielhansen.github.io/genbioconductor/html/Biostrings_Matching.html

Example:

suppressPackageStartupMessages(library(Biostrings))
dnaseq <- DNAString("ATAGCCATGATGATTTAACCAGGTCATTT") # the sequence
motif <- DNAStringSet(c("ATG", "TGA")) # the motifs
pos <- matchPDict(motif, dnaseq)
pos
#> MIndex object of length 2
#> [[1]]
#> IRanges object with 2 ranges and 0 metadata columns:
#>           start       end     width
#>       <integer> <integer> <integer>
#>   [1]         7         9         3
#>   [2]        10        12         3
#> 
#> [[2]]
#> IRanges object with 2 ranges and 0 metadata columns:
#>           start       end     width
#>       <integer> <integer> <integer>
#>   [1]         8        10         3
#>   [2]        11        13         3
start(pos) # ATG starts at pos 7 and 10; TGA at 8 and 11 
#> IntegerList of length 2
#> [[1]] 7 10
#> [[2]] 8 11
countPDict(motif, dnaseq)
#> [1] 2 2

# search reverse complement:
matchPDict(reverseComplement(motif), dnaseq)
#> MIndex object of length 2
#> [[1]]
#> IRanges object with 2 ranges and 0 metadata columns:
#>           start       end     width
#>       <integer> <integer> <integer>
#>   [1]         6         8         3
#>   [2]        25        27         3
#> 
#> [[2]]
#> IRanges object with 1 range and 0 metadata columns:
#>           start       end     width
#>       <integer> <integer> <integer>
#>   [1]        24        26         3

^{Created on 2020-08-05 by the reprex package (v0.3.0)}