Finding Complete and Overlapped ORFs

The main function in the GeneFinder package is findorfs, which serves as an interface to various gene-finding algorithms. All methods return an ORFCollection—a structure that bundles the found ORFs with their source sequence, providing a clean API for sequence extraction.

Note

The minlen keyword argument is set to a minimum length of 6 nucleotides (nt). As a result, it may identify short ORFs that aren't necessarily genes, such as dna"ATGTGA" producing the amino acid sequence aa"M*".

Usage Example

Here's an example of using findorfs with the NaiveFinder algorithm:

julia> using BioSequences, GeneFinder

julia> seq = dna"AACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAACAGCACTGGCAATCTGACTGTGGGCGGTGTTACCAACGGCACTGCTACTACTGGCAACATCGCACTGACCGGTAACAATGCGCTGAGCGGTCCGGTCAATCTGAATGCGTCGAATGGCACGGTGACCTTGAACACGACCGGCAATACCACGCTCGGTAACGTGACGGCACAAGGCAATGTGACGACCAATGTGTCCAACGGCAGTCTGACGGTTACCGGCAATACGACAGGTGCCAACACCAACCTCAGTGCCAGCGGCAACCTGACCGTGGGTAACCAGGGCAATATCAGTACCGCAGGCAATGCAACCCTGACGGCCGGCGACAACCTGACGAGCACTGGCAATCTGACTGTGGGCGGCGTCACCAACGGCACGGCCACCACCGGCAACATCGCGCTGACCGGTAACAATGCACTGGCTGGTCCTGTCAATCTGAACGCGCCGAACGGCACCGTGACCCTGAACACAACCGGCAATACCACGCTGGGTAATGTCACCGCACAAGGCAATGTGACGACTAATGTGTCCAACGGCAGCCTGACAGTCGCTGGCAATACCACAGGTGCCAACACCAACCTGAGTGCCAGCGGCAATCTGACCGTGGGCAACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAGC";

julia> collection = findorfs(seq, finder=NaiveFinder)
ORFCollection{NaiveFinder} with 12 ORFs in 726bp sequence:
 ORF{NaiveFinder}(29:40, '+', 2)
 ORF{NaiveFinder}(137:145, '+', 2)
 ORF{NaiveFinder}(164:184, '+', 2)
 ⋮

Working with ORFCollections

The ORFCollection provides a convenient interface for working with ORFs:

julia> collection[1]  # First ORF
ORF{NaiveFinder}(29:40, '+', 2)

julia> collection[1:5]  # Range of ORFs (returns a Vector)
5-element Vector{OpenReadingFrame{NaiveFinder}}:
 ORF{NaiveFinder}(29:40, '+', 2)
 ⋮

julia> length(collection)  # Number of ORFs
12

julia> source(collection)  # Access source sequence
726nt DNA Sequence:
AACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTG…GCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAGC

Extracting Sequences from ORFs

Extract sequences using the sequence function with an index or ORF:

julia> sequence(collection, 1)  # By index
12nt DNA Sequence:
ATGCAACCCTGA

julia> orf = collection[1]; sequence(collection, orf)  # By ORF
12nt DNA Sequence:
ATGCAACCCTGA

julia> sequence.(Ref(collection), collection.orfs)  # All sequences using broadcasting
12-element Vector{LongSubSeq{DNAAlphabet{4}}}:
 ATGCAACCCTGA
 ATGCGCTGA
 ⋮

Translating ORF Sequences

To translate ORF sequences to amino acids, use BioSequences.translate on extracted sequences:

julia> using BioSequences

julia> translate(sequence(collection, 1))
4aa Amino Acid Sequence:
MQP*

julia> translate.(sequence.(Ref(collection), collection.orfs))  # Translate all ORFs
12-element Vector{LongAA}:
 MQP*
 MR*
 MRRMAR*
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