Introduction to GenBank Files

• GenBank is a widely used format for storing and exchanging biological sequence data.
• It contains information about the sequence, features, references, and more.

Parsing GenBank Files

• Biopython provides the SeqIO module for parsing GenBank files.
• SeqIO allows easy access to sequence records and their associated information.

Reading GenBank Files

from Bio import SeqIO

genbank_file = "sequence.gb"

for record in SeqIO.parse(genbank_file, "genbank"):
    print("Sequence ID:", record.id)
    print("Sequence Description:", record.description)
    print("Sequence Features:", record.features)

• Read a GenBank file using the SeqIO.parse() function.
• Iterate over each record in the file.
• Access the ID, description, and features of each sequence record.
• Print the sequence ID, description, and features.

Accessing Sequence Features

from Bio import SeqIO

genbank_file = "sequence.gb"

for record in SeqIO.parse(genbank_file, "genbank"):
    for feature in record.features:
        print("Feature Type:", feature.type)
        print("Feature Location:", feature.location)
        print("Feature Qualifiers:", feature.qualifiers)

• Read a GenBank file using the SeqIO.parse() function.
• Iterate over each record in the file.
• Iterate over each feature in the record.
• Access the type, location, and qualifiers of each feature.
• Print the feature type, location, and qualifiers.

Extracting Sequence Data

from Bio import SeqIO

genbank_file = "sequence.gb"

for record in SeqIO.parse(genbank_file, "genbank"):
    sequence = record.seq
    print("Sequence Data:", sequence)

• Read a GenBank file using the SeqIO.parse() function.
• Iterate over each record in the file.
• Access the sequence data of each record.
• Print the sequence data.

Manipulating GenBank Records

• Biopython provides various methods and attributes to manipulate GenBank records.
• These include adding features, modifying sequence data, and updating metadata.

Modifying Sequence Data

from Bio import SeqIO

genbank_file = "sequence.gb"

for record in SeqIO.parse(genbank_file, "genbank"):
    # Modify the sequence data
    record.seq = record.seq.lower()

    # Update the description
    record.description += " (modified)"

    # Write the modified record to a new file
    output_file = "modified_sequence.gb"
    SeqIO.write(record, output_file, "genbank")

    print("Modified GenBank file written to:", output_file)

• Read a GenBank file using the SeqIO.parse() function.
• Modify the sequence data by converting it to lowercase.
• Update the description by appending “(modified)” to it.
• Write the modified record to a new GenBank file using SeqIO.write().
• Print the name of the output file.

Summary

• Parsing GenBank files allows easy access to sequence records and their features.
• Biopython’s SeqIO module provides functionalities for reading, manipulating, and writing GenBank files.
• Understanding the structure and contents of GenBank files is crucial for effective bioinformatics analysis.