Finding complete and overlapped ORFIs

The main function in the GeneFinder package is findorfs, which serves as an interface to various gene-finding algorithms. By default, findorfs uses a NaiveFinder algorithm, a simple approach that detects all non-outbounded Open Reading Frames (ORFs) in a DNA sequence. You can also specify a different algorithm by setting the finder keyword argument. For more details on the NaiveFinder algorithm, see NaiveFinder documentation for more details.

Note

The minlen keyword argument in NaiveFinder 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 to identify ORFs in a DNA sequence:

julia> using BioSequences, GeneFinder

# > 180195.SAMN03785337.LFLS01000089 -> finds only 1 gene in Prodigal (from Pyrodigal tests)
seq = dna"AACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAACAGCACTGGCAATCTGACTGTGGGCGGTGTTACCAACGGCACTGCTACTACTGGCAACATCGCACTGACCGGTAACAATGCGCTGAGCGGTCCGGTCAATCTGAATGCGTCGAATGGCACGGTGACCTTGAACACGACCGGCAATACCACGCTCGGTAACGTGACGGCACAAGGCAATGTGACGACCAATGTGTCCAACGGCAGTCTGACGGTTACCGGCAATACGACAGGTGCCAACACCAACCTCAGTGCCAGCGGCAACCTGACCGTGGGTAACCAGGGCAATATCAGTACCGCAGGCAATGCAACCCTGACGGCCGGCGACAACCTGACGAGCACTGGCAATCTGACTGTGGGCGGCGTCACCAACGGCACGGCCACCACCGGCAACATCGCGCTGACCGGTAACAATGCACTGGCTGGTCCTGTCAATCTGAACGCGCCGAACGGCACCGTGACCCTGAACACAACCGGCAATACCACGCTGGGTAATGTCACCGCACAAGGCAATGTGACGACTAATGTGTCCAACGGCAGCCTGACAGTCGCTGGCAATACCACAGGTGCCAACACCAACCTGAGTGCCAGCGGCAATCTGACCGTGGGCAACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAGC"

orfs = findorfs(seq, finder=NaiveFinder) # use finder=NaiveCollector as an alternative

12-element Vector{ORFI{4, NaiveFinder}}:
 ORFI{NaiveFinder}(29:40, '+', 2)
 ORFI{NaiveFinder}(137:145, '+', 2)
 ORFI{NaiveFinder}(164:184, '+', 2)
 ORFI{NaiveFinder}(173:184, '+', 2)
 ORFI{NaiveFinder}(236:241, '+', 2)
 ORFI{NaiveFinder}(248:268, '+', 2)
 ORFI{NaiveFinder}(362:373, '+', 2)
 ORFI{NaiveFinder}(470:496, '+', 2)
 ORFI{NaiveFinder}(551:574, '+', 2)
 ORFI{NaiveFinder}(569:574, '+', 2)
 ORFI{NaiveFinder}(581:601, '+', 2)
 ORFI{NaiveFinder}(695:706, '+', 2)

Extracting Sequences from ORFIs

The ORFI structure displays the location, frame, and strand, and other fields (see more about the OpenReadingFrameInterval struct). To extract the sequence of an ORFI instance, you can use the sequence method directly on it, or you can also broadcast it over the orfs collection using the dot syntax .:

julia> sequence.(orfs)

12-element Vector{LongSubSeq{DNAAlphabet{4}}}:
 ATGCAACCCTGA
 ATGCGCTGA
 ATGCGTCGAATGGCACGGTGA
 ATGGCACGGTGA
 ATGTGA
 ATGTGTCCAACGGCAGTCTGA
 ATGCAACCCTGA
 ATGCACTGGCTGGTCCTGTCAATCTGA
 ATGTCACCGCACAAGGCAATGTGA
 ATGTGA
 ATGTGTCCAACGGCAGCCTGA
 ATGCAACCCTGA

Translating ORFIs to Amino Acid Sequences

Similarly, you can extract the amino acid sequences of the ORFIs using the translate function.

julia> translate.(orfs)

12-element Vector{LongAA}:
 MQP*
 MR*
 MRRMAR*
 MAR*
 M*
 MCPTAV*
 MQP*
 MHWLVLSI*
 MSPHKAM*
 M*
 MCPTAA*
 MQP*

This returns a vector of translated amino acid sequences, allowing for easy interpretation of each ORF's potential protein product.