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]