NCBI Sequence Fetcher

This is a Python script that fetches sequences from a database using the Bio.Entrez library.

This work was proposed in the Curricular Unit of Biology Analysis and Sequences of the bioinformatics course https://stuntspt.gitlab.io/ASB/classes/class_05/index.html#/

Requisites

• Python
• Bio.Entrez library

Installation

Biopython

pip install biopython

Usage

python fetch_sequences.py [database name] [search term]

Where [database name] is the name of the database you want to search (e.g., "nucleotide" for the NCBI nucleotide database), and [search term] is the term you want to search for.

Examples

To search the NCBI nucleotide database for sequences related to "E. coli", run:

python fetch_sequences.py nucleotide "Escherichia coli"

This will fetch the sequences in batches and print them to the console.

Credits

This script uses the Bio.Entrez library from the Biopython project.

License

MIT License