Problem 1: Use Biopython to download 10 influenza hemagglutinin sequences like we did in the Class 21 worksheet. Print the list of genbank identifiers, then fetch and save all of the records to a file called "influenza_HA.gb".
# You will need Entrez and Medline to solve this problem from Bio import Entrez, SeqIO Entrez.email = "firstname.lastname@example.org" # let's do a search for influenza H1N1 viruses from Texas handle = Entrez.esearch(db="nucleotide", # database to search term="influenza a virus texas h1n1 hemagglutinin complete cds", # search term retmax=10 # number of results that are returned ) record = Entrez.read(handle) handle.close() gi_list = record["IdList"] # list of genbank identifiers found print(gi_list) # Fetch records from the database handle = Entrez.efetch(db="nucleotide", id=gi_list, rettype="gb", retmode="text") data = handle.read() handle.close() # close the handle # Write data to a file with open("influenza_HA.gb", "w") as outfile: outfile.write(data)
['930625975', '614460113', '614459483', '908275045', '908274326', '908274263', '428231228', '224022022', '400315744', '676287366']
Problem 2: Restriction enzymes cut DNA by recognizing specific motifs (patterns in the DNA sequence usually less than 10 nucleotides). Some restriction enzymes recognize degenerate motifs. That is, they recognize multiple motifs that differ by only 1 or 2 nucleotides.
Using your sequence file from Problem 1 and regular expressions, determine if any of the influenza sequences contain the following restriction sites:
import re # Your code goes here # Open the genbank file with flu sequences in_handle = open("influenza_HA.gb", "r") records = SeqIO.parse(in_handle, "genbank") # Start counters for EcoRI and BisI restriction sites eco_count = 0 bis_count = 0 # Loop over each sequence for record in records: # Match match_eco = re.search(r"GAATTC", str(record.seq)) match_bis = re.search(r"GC[ATCG]GC", str(record.seq)) if match_eco: eco_count += 1 if match_bis: bis_count += 1 # Remember to close the file handle! in_handle.close() print("There are EcoRI restriction sites in", eco_count, "sequences.") print("There are BisI restriction sites in", bis_count, "sequences.")
There are EcoRI restriction sites in 3 sequences. There are BisI restriction sites in 10 sequences.