Hello! We are currently working with a seaweed genome, linked below: https://www.ncbi.nlm.nih.gov/assembly/GCA_002049455.2/
What we are looking to do is translate the genome DNA file into the six possible amino acid sequences (six reading frames), without identifying open reading frames. Due to the size of the genome file, we have been unable to successfully produce the six-frame translations using desktop applications and online resources, and are hoping that a program could be made and run in MATLAB that would produce the 6 frame translations for the entire genome file.
Using BioPython you can get the translated reading frames from the GenBank files using something like the following:
from Bio.Seq import Seq
from Bio import SeqIO
record_iterator = SeqIO.parse("/path/to/GCA_002049455.2_P_umbilicalis_v1_genomic.fna", "fasta")
translate_0 = []
translate_1 = []
translate_2 = []
translate_0rc = []
translate_1rc = []
translate_2rc = []
for record in record_iterator:
translate_0.append(record.seq[:].translate())
translate_1.append(record.seq[1:].translate())
translate_2.append(record.seq[2:].translate())
translate_0rc.append(record.seq[:].reverse_complement().translate())
translate_1rc.append(record.seq[:-1].reverse_complement().translate())
translate_2rc.append(record.seq[:-2].reverse_complement().translate())
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