findORFs {ORFik}R Documentation

Find Open Reading Frames.

Description

Find all Open Reading Frames (ORFs) on the input sequences in ONLY 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 = TRUE,
  minimumLength = 0)

Arguments

seqs

(DNAStringSet or character) DNA sequences to search for Open Reading Frames. Can be both uppercase or lowercase. Easiest call to get seqs if you want only regions from a fasta/fasta index pair is: seqs = ORFik:::txSeqsFromFa(grl, faFile), where grl is a GRanges/List of regions.

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 TRUE. Keep only the longest ORF per unique (seqname, strand, stopcodon) combination, you can also use function longestORFs after creation of ORFs for same result.

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 = 30 bases. Use this param to restrict search.

Details

If you want antisence strand too, do: #positive strands pos <- findORFs(seqs) #negative strands (DNAStringSet only if character) neg <- findORFs(reverseComplement(DNAStringSet(seqs))) relist(c(GRanges(pos, strand = "+"), GRanges(neg, strand = "-")), skeleton = merge(pos, neg))

Value

(IRangesList) of ORFs locations by START and STOP sites grouped by input seqeunces. In a list of sequences, only the indices of the sequences that had ORFs will be returned, e.g. 3 sequences where only 1 and 3 has ORFs, will return size 2 IRangesList with names c("1", "3"). If there are a total of 0 ORFs, an empty IRangesList will be returned.

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 1.2.1 Index]