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What is the length of the longest ORF appearing in reading frame 2 of any of the sequences?

Dear bioinformatician or similar, I am new to Python programming and I have to answer this question: "What is the length of the longest ORF appearing in reading frame 2 of any of the sequences?" I attached the result but I want to customize/change the code so that I could specify ORF appearing just in the reading frame 2.

#######################
from Bio import SeqIO
from Bio.Seq import Seq
#Build a Dictionary
sequences = {record.id: record.seq for record in SeqIO.parse(seq, "fasta")}  

max_length_in_frame2 = 0
longest_orf_seq_in_frame2 = ""


for seq_id, sequence in sequences.items():
    # Create a Seq object and translate it to protein, specifying the frame
    protein_seq_frame2 = sequence.translate()   # Frame 1 is the 3rd reading frame (0-indexed)


    # Split the protein sequence into ORFs by stop codons (*)
    potential_ors = protein_seq_frame2.split("*")

    for orf in potential_ors:
        # Check if the ORF starts with a start codon (M)
        #if orf.startswith("M"):
            # Find the length of the ORF
            orf_length = len(orf)
            # Keep track of the longest ORF found in frame 2 so far
            if orf_length > max_length_in_frame2:
                max_length_in_frame2 = orf_length
                longest_orf_seq_in_frame2 = orf

print(f"The longest ORF in reading frame 2 is {max_length_in_frame2} amino acids long.")
print(f"The sequence is: {longest_orf_seq_in_frame2}")
#####################################

Thanks in advance, Francesco

python
• 973 views • link
written by fra.r.silvestro • fra.r.silvestro

Generally speaking, we are not here to provide code review service and/or fix code for what appears to be a school assignment. If you have a specific question, especially if not related to assignments, I think you may be more likely to get some feedback. It would also be helpful to format the code properly.

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

1 answer

I suppose that this is a good resolution:

frame = 2
protein_seq_frame2 = sequence[frame -1:]
protein_seq_frame3 = protein_seq_frame2.translate()
• 0 views • link
written by fra.r.silvestro • fra.r.silvestro

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