findORFs: Find Open Reading Frames.

In JokingHero/ORFik: Open Reading Frames in Genomics

Find Open Reading Frames.

Description

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.

Usage

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

Arguments

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. Note: Remember that if you extracted through a GRanges object, that must have been sorted with negative strand exons descending.
startCodon	(character vector) Possible START codons to search for. Check startDefinition for helper function. Note that it is case sensitive, so "atg" would give 0 hits for a sequence with only capital "ATG" ORFs.
stopCodon	(character vector) Possible STOP codons to search for. Check stopDefinition for helper function. Note that it is case sensitive, so "tga" would give 0 hits for a sequence with only capital "TGA" ORFs.
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.

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 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.

See Also

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

Examples

## 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")) # 1 ORF per transcript

## 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
# Save as .fasta (orf_seqs must be of type DNAStringSet)
# writeXStringSet(orf_seqs, "orfs.fasta")
## Reading from file and find ORFs
#findORFs(readDNAStringSet("path/to/transcripts.fasta"))

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.