Biopython search based on accession number

When working with biological data, it is often necessary to search for specific sequences based on their accession numbers. Biopython is a powerful library that provides various tools for working with biological data in Python. In this article, we will explore three different ways to perform a Biopython search based on accession number.

Option 1: Using Entrez

One way to perform a Biopython search based on accession number is by using the Entrez module. Entrez is a powerful tool that allows you to access various biological databases, including the NCBI nucleotide database.

from Bio import Entrez

def search_by_accession(accession):
    Entrez.email = "your_email@example.com"
    handle = Entrez.efetch(db="nucleotide", id=accession, rettype="fasta", retmode="text")
    record = handle.read()
    handle.close()
    return record

accession_number = "NC_000913.3"
sequence = search_by_accession(accession_number)
print(sequence)

In this code, we first import the Entrez module from Biopython. We then define a function called search_by_accession that takes an accession number as input. Inside the function, we set our email address using the Entrez.email attribute, which is required by NCBI. We then use the Entrez.efetch function to retrieve the sequence record for the given accession number from the nucleotide database. Finally, we return the sequence record and print it.

Option 2: Using SeqIO

Another way to perform a Biopython search based on accession number is by using the SeqIO module. SeqIO is a module in Biopython that provides a simple interface for reading and writing sequence files in various formats.

from Bio import SeqIO

def search_by_accession(accession):
    record = SeqIO.read(accession + ".fasta", "fasta")
    return record.seq

accession_number = "NC_000913.3"
sequence = search_by_accession(accession_number)
print(sequence)

In this code, we first import the SeqIO module from Biopython. We then define a function called search_by_accession that takes an accession number as input. Inside the function, we use the SeqIO.read function to read the sequence record from a FASTA file with the same name as the accession number. Finally, we return the sequence and print it.

Option 3: Using E-utilities

The third way to perform a Biopython search based on accession number is by using the E-utilities. The E-utilities are a set of eight server-side programs that provide a consistent interface to the NCBI databases.

from Bio import Entrez

def search_by_accession(accession):
    Entrez.email = "your_email@example.com"
    handle = Entrez.efetch(db="nucleotide", id=accession, rettype="fasta", retmode="text")
    record = handle.read()
    handle.close()
    return record

accession_number = "NC_000913.3"
sequence = search_by_accession(accession_number)
print(sequence)

In this code, we use the same approach as in Option 1, which is using the Entrez module to perform the search based on accession number. The only difference is that we set the email address using the Entrez.email attribute.

After exploring these three options, it is clear that Option 1 and Option 3 are essentially the same, as they both use the Entrez module to perform the search. Option 2, on the other hand, uses the SeqIO module to read the sequence record from a FASTA file. While all three options are valid, Option 1 and Option 3 are more versatile as they allow you to directly retrieve the sequence record from the NCBI database without the need for a separate FASTA file. Therefore, Option 1 and Option 3 are the better options for performing a Biopython search based on accession number.

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