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Python script to extract a protein sequence from a genome using a General Feature Format (GFF) file !
By LEGE 296 days ago
#You typically need the corresponding genome sequence file in FASTA format. The GFF file contains information about the #features (such as genes) in the genome, including their locations and annotations.
#The outline of the steps :
#Parse the GFF file to extract information about the gene locations.
#Use the gene locations to extract the corresponding DNA sequences from the genome in FASTA format.
#Translate the DNA sequences into protein sequences.
#Simple example using Python and Biopython
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
def extract_protein_sequence(gff_file, genome_fasta, gene_id):
# Step 1: Parse the GFF file
gene_locations = {}
with open(gff_file, 'r') as gff:
for line in gff:
if not line.startswith('#'):
fields = line.strip().split('\t')
if fields[2] == 'gene':
gene_id = fields[8].split(';')[0].split('=')[1]
gene_locations[gene_id] = (int(fields[3]), int(fields[4]))
# Step 2: Extract DNA sequence from the genome
genome_record = SeqIO.read(genome_fasta, 'fasta')
gene_start, gene_end = gene_locations[gene_id]
gene_dna_sequence = genome_record.seq[gene_start - 1:gene_end]
# Step 3: Translate DNA sequence into protein sequence
gene_protein_sequence = gene_dna_sequence.translate()
return gene_protein_sequence
# Example usage
gff_file = 'path/to/your/file.gff'
genome_fasta = 'path/to/your/genome.fasta'
gene_id_to_extract = 'your_gene_id'
protein_sequence = extract_protein_sequence(gff_file, genome_fasta, gene_id_to_extract)
print(protein_sequence)
