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]