BLAST with Biopython: Integrating BLAST Searches into Data Science Projects

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BLAST, or Basic Local Alignment Search Tool, is a powerful and widely used bioinformatics tool for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotide sequences of DNA. The main purpose of BLAST is to identify sequences in a database that are similar to a query sequence, thereby providing insights into the functional and evolutionary relationships between different sequences.

Here are key aspects of BLAST:

I. Types of BLAST:

These scripts send the BLAST queries to the NCBI server, retrieve the results, and save them in XML format. You can then parse the XML results using Biopython’s Bio.Blast.NCBIXML module to extract relevant information.

1. BLASTP:

• Compares an amino acid query sequence against a protein sequence database.

from Bio.Blast import NCBIWWW

# Replace 'YOUR_QUERY_SEQUENCE' with your actual protein sequence
query_sequence = "YOUR_QUERY_SEQUENCE"

# Perform BLASTP search
result_handle = NCBIWWW.qblast("blastp", "nr", query_sequence)

# Save the result
with open("blastp_result.xml", "w") as result_file:
    result_file.write(result_handle.read())

result_handle.close()