Objective

• Understand the concept and significance of biological databases in bioinformatics.
• Explore different types of biological databases and their applications.
• Learn how to access and retrieve data from biological databases using Biopython.

Introduction to Biological Databases:

• Biological databases store and organize vast amounts of biological data, such as DNA sequences, protein structures, and gene annotations.
• They serve as valuable resources for researchers, providing access to a wide range of biological information.

Types of Biological Databases:

1. Sequence Databases (e.g., GenBank, UniProt)
2. Structure Databases (e.g., Protein Data Bank, PDB)
3. Gene Expression Databases (e.g., GEO, ArrayExpress)
4. Pathway Databases (e.g., KEGG, Reactome)
5. Functional Annotation Databases (e.g., Gene Ontology, GO)

Importance of Biological Databases:

• Biological databases facilitate data storage, retrieval, and analysis, enabling researchers to make discoveries and gain insights.
• They support various bioinformatics tasks, including sequence alignment, protein structure prediction, and functional annotation.

Accessing Biological Databases with Biopython:

• Biopython provides modules and functions to access and retrieve data from various biological databases.
• It offers a unified interface to query databases and extract relevant information.

Using Biopython to Access Sequence Databases

from Bio.PDB import PDBList

# Create a PDBList object
pdblist = PDBList()

# Download a PDB file
pdblist.retrieve_pdb_file("1abc")

# Access the downloaded PDB file
pdb_file = "pdb1abc.ent"

# Parse the PDB file using Bio.PDB
parser = PDBParser()
structure = parser.get_structure("1abc", pdb_file)

# Access and analyze the structure
model = structure[0]
chain = model['A']
residue = chain[1]
atoms = residue.get_atoms()

• Create a PDBList object from Bio.PDB to access the Protein Data Bank (PDB).
• Use retrieve_pdb_file() to download a specific PDB file (e.g., “1abc”).
• Specify the PDB identifier (e.g., “1abc”) to access the downloaded file.
• Parse the PDB file using PDBParser() from Bio.PDB.
• Access and analyze the structure components (model, chain, residue, atoms).

Summary

• Biological databases are crucial resources for storing and accessing biological data.
• Biopython provides modules and functions to query and retrieve data from various biological databases.
• Explore the functionality of Biopython to access sequence databases, structure databases, and other biological data resources.