Introduction to Sequence Objects:

• Biopython represents biological sequences using sequence objects.
• Sequence objects encapsulate the sequence data along with associated metadata and provide convenient methods for sequence manipulation.

Properties of Sequence Objects:

• Sequence objects have various properties and attributes that provide valuable information about the sequence.

Accessing Sequence Data

• The Seq object provides the seq attribute to access the sequence data as a string.

from Bio.Seq import Seq

sequence = Seq("ATCGATCGATCG")
sequence_data = sequence.seq

print("Sequence Data:", sequence_data)

• Create a Seq object from a DNA sequence.
• Access the sequence data using the seq attribute.
• Print the sequence data.

Accessing Sequence Length

• The len() function can be used to obtain the length of a sequence object.

from Bio.Seq import Seq

sequence = Seq("ATCGATCGATCG")
sequence_length = len(sequence)

print("Sequence Length:", sequence_length)

• Create a Seq object from a DNA sequence.
• Use the len() function to calculate the length of the sequence object.
• Print the sequence length.

Accessing Sequence Alphabet

• The alphabet attribute provides information about the type of sequence (e.g., DNA, RNA, protein).

from Bio.Seq import Seq

sequence = Seq("ATCGATCGATCG")
sequence_alphabet = sequence.alphabet

print("Sequence Alphabet:", sequence_alphabet)

• Create a Seq object from a DNA sequence.
• Access the sequence alphabet using the alphabet attribute.
• Print the sequence alphabet.

Accessing Sequence Metadata

• Sequence objects can store additional metadata such as ID, description, and name.

from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord

sequence = Seq("ATCGATCGATCG")
sequence_id = "Seq1"
sequence_description = "Sample sequence"

sequence_record = SeqRecord(sequence, id=sequence_id, description=sequence_description)

print("Sequence ID:", sequence_record.id)
print("Sequence Description:", sequence_record.description)

• Create a Seq object from a DNA sequence.
• Define the sequence ID and description.
• Create a SeqRecord object with the sequence and metadata.
• Access the ID and description properties of the SeqRecord object.
• Print the sequence ID and description.

Summary

• Sequence objects in Biopython encapsulate the sequence data along with metadata.
• Sequence properties and attributes provide useful information about the sequence, such as the sequence data, length, alphabet, and metadata.
• Understanding sequence objects and their properties is essential for efficient sequence manipulation and analysis.