Open Reading Frames (ORF) finder using regeC.

In this code, we defined an ORF as:

• Start condition: codon "ATG"
• Stop condition: codon "TAA" or "TAG" or "TGA" or the end of the sequence is reached.
• The length is a multiple of 3.
• An ORF can contain multiple start codons "ATG" but only one stop codon "TAA" or "TAG" or "TGA".
• Within the same frame, if an ORF is completely contained in a larger one, then we don't consider it.

ECemple:

input: GAGATCAGCTTTTGTTCAGAACCTGCGGCCGCTGAGGAGACGGTGACCTGGGTCCCCTGGCCCCAACAGTCCCTCTGATCGACTATCGGATCTCTGGCACAGTAATACACGGCCGTGTCCTCAGGGGTCACAGAGCTCAGCTGCAGGGAGAACTGGTTCTTGGACGTGTCCCTGGAGATGGAAGTGCGACTCTTGAGGGATGGACTGTAGTAAGTGCTGCCATCATAAGCTATGACTCCCATCCACTCCAGCCCCTTCCCTGAGGGCTGGCGGATCCAGCTCCAAGTATAATAGCTGGTTGTGATGGAGCCACCAGAGAAAGTGCAGGTGAGGGAGAGCGTCTGCGAGGGCTTCACCAGACTGGACCAGCTGCACCTGGGCCATGGCCGGCTGAGCTGCCAGCAGCAGCAA

min_dna_len = 30

output:

STRAND 1:
        frame 1
                start_pos: 178, stop_pos: 210,  seq_protein: MEVRLLRDGL*
                start_pos: 232, stop_pos: 291,  seq_protein: MTPIHSSPFPEGCRIQLQV*
                start_pos: 304, stop_pos: 411,  seq_protein: MEPPEKVQVRESVCEGFTRLDQLHLGHGRLSCQQQQ
        frame 2
                start_pos: 200, stop_pos: 235,  seq_protein: MDCSKCCHHKL*

STRAND -1:
        frame 3
                start_pos: 384, stop_pos: 223,  seq_protein: MAQVQLVQSGEALADALPHLHFLCCLHHNQLLYLELDPPALREGAGVDGSHSL*
        frame 2
                start_pos: 242, stop_pos: 3,    seq_protein: MGVIAYDGSTYYSPSLKSRTSISRDTSKNQFSLQLSSVTPEDTAVYYCARDPIVDQRDCCGQGTQVTVSSAAAGSEQKLI
        frame 1
                start_pos: 226, stop_pos: 137,  seq_protein: MMAALTTVHPSRVALPSPGTRPRTSSPCS*

The results for this input are the same as those obtained from https://www.ncbi.nlm.nih.gov/orffinder/