Find potential open reading frames (ORFs) in a DNA sequence.

By Coghlan (2011) A little book of R for bioinformatics. https://a-little-book-of-r-for-bioinformatics.readthedocs.io/en/latest/. Originally called findORFsinSeq()

find_ORFs_in_seq(sq)

Arguments

sq

Input sequence

Examples


# From Coglan 2011
## Toy example
s1 <- "aaaatgcagtaacccatgccc"
find_ORFs_in_seq(s1)

#> $orfstarts
#> [1] 4
#> 
#> $orfstops
#> [1] 12
#> 
#> $orflengths
#> [1] 9
#> 

## Dengue virus example
data(dengueseqstartstring)
find_ORFs_in_seq(dengueseqstartstring)

#> $orfstarts
#> [1] 298 318
#> 
#> $orfstops
#> [1] 480 371
#> 
#> $orflengths
#> [1] 183  54
#>