Function to identify potential start and stop codons

By Coghlan (2011) A little book of R for bioinformatics. https://a-little-book-of-r-for-bioinformatics.readthedocs.io/en/latest/src/chapter7.html. The functions was originally named findPotentialStartsAndStops().

find_start_stop_codons(sq)

Arguments

sq	DNA sequence

Details

Searches a DNA sequence using Biostrings::matchPattern(codon, sequence) to look for start and stop codons. Currently only uses the standard genetic code.

Examples

# Example sequence from Coghlan 2011
s1 <- "aaaatgcagtaacccatgccc"

# Returns a list with 2 elements
## 1) locations of codons
## 2) The codon
find_start_stop_codons(s1)
#> $positions
#> [1]  4 10 16
#> 
#> $types
#> [1] "atg" "taa" "atg"
#>