findORFs: Find Open Reading Frames.
In ORFik: Open Reading Frames in Genomics

Description Usage Arguments Details Value See Also Examples

Find all Open Reading Frames (ORFs) on the simple input sequences in ONLY 5'- 3' direction (+), but within all three possible reading frames. Do not use findORFs for mapping to full chromosomes, then use findMapORFs! 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.

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

`seqs`	(DNAStringSet or character vector) - DNA/RNA 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 search regions and faFile is a `FaFile`.
`startCodon`	(character vector) Possible START codons to search for. Check `startDefinition` for helper function.
`stopCodon`	(character vector) Possible STOP codons to search for. Check `stopDefinition` for helper function.
`longestORF`	(logical) Default TRUE. Keep only the longest ORF per unique stopcodon: (seqname, strand, stopcodon) combination, Note: Not longest per transcript! You can also use function `longestORFs` after creation of ORFs for same result.
`minimumLength`	(integer) Default is 0. Which is START + STOP = 6 bp. Minimum length of ORF, without counting 3bps 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.

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))

(IRangesList) of ORFs locations by START and STOP sites grouped by input sequences. 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.

Other findORFs: findMapORFs(), findORFsFasta(), findUORFs(), startDefinition(), stopDefinition()

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

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

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

## Get DNA sequences from ORFs
seq <- DNAStringSet(c("ATGTAA", "AAA", "ATGATGTAA"))
names(seq) <- c("tx1", "tx2", "tx3")
orfs <- findORFs(seq, longestORF = FALSE)

#  you can get sequences like this:
gr <- unlist(orfs, use.names = TRUE)
gr <- GRanges(seqnames = names(seq)[as.integer(names(gr))],
 ranges(gr), strand = "+")
# Give them some proper names:
names(gr) <- paste0("ORF_", seq.int(length(gr)), "_", seqnames(gr))
orf_seqs <- getSeq(seq, gr)
orf_seqs
# Convert to DNA DNAStringSet and Save as .fasta
# writeXStringSet(orf_seqs, "orfs.fasta")
## Reading from file and find ORFs