findORFs {ORFik} | R Documentation

## Find Open Reading Frames.

### Description

Find all Open Reading Frames (ORFs) on the input sequences in 5'- 3' direction, but within all three possible reading frames. For each sequence of the input vector `IRanges` with START and STOP positions (inclusive) will be returned as `IRangesList`. Returned coordinates are relative to the input sequences.

### Usage

    findORFs(seqs, startCodon = startDefinition(1),
      stopCodon = stopDefinition(1), longestORF = FALSE, minimumLength = 0)

### Arguments

`seqs` | (DNAStringSet or character) DNA sequences to search for Open Reading Frames.
`startCodon` | (character) Possible START codons to search for. Check [startDefinition()] for helper function.
`stopCodon` | (character) Possible STOP codons to search for. Check [stopDefinition()] for helper function.
`longestORF` | (logical) Default FALSE. When TRUE will only report ORFs that are longest, all smaller overlapping ORFs will be ignored. When FALSE will report all possible ORFs in all three reading frames.
`minimumLength` | (integer) Default is 0. Minimum length of ORF, without counting 3bp for START and STOP codons. For example minimumLength = 8 will result in size of ORFs to be at least START + 8*3 (bp) + STOP. Use this param to restrict search.

### Value

(IRangesList) of ORFs locations incuding START and STOP codons grouped by input seqeunces.

### See Also

[findMapORFs()], [findORFsFasta()], [startDefinition()], [stopDefinition()]

Other findORFs: `findMapORFs`, `findORFsFasta`, `startDefinition`, `stopDefinition`

### Examples

    findORFs("ATGTAA")
    findORFs("ATGTTAA") # not in frame anymore

    findORFs("ATGATGTAA") # two ORFs
    findORFs("ATGATGTAA", longestORF = TRUE) # only longest of two above

    findORFs(c("ATGTAA", "ATGATGTAA"))

[Package ORFik version 1.0.0 Index]