Biopython Practice Scripts & Sequence Analysis Exercises

This repository contains a collection of small Python scripts created while learning and practising Biopython and fundamental bioinformatics operations. Each script focuses on a specific task—such as reading FASTA files, parsing GenBank records, translating sequences, computing nucleotide frequencies, retrieving sequences from NCBI Entrez, and more.

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Features

• Read and parse FASTA files
• Read and process GenBank files
• Work with Seq and SeqRecord objects
• Translate DNA → Protein
• Extract ORFs and codon frames
• Retrieve sequences using NCBI Entrez API
• Calculate GC content, nucleotide frequencies
• Work with multiple FASTA files
• Simple search and filtering operations
• Practice scripts for fundamental bioinformatics logic

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📁 Repository Structure

File Name	Description
1.Bio.Seq.py	Basic Seq object operations
10.SeqRecord.py	Creating and modifying SeqRecord objects
11.seq_record.py	Working with metadata in SeqRecord
12.fasta_read.py	Reading FASTA files with Biopython
13.Read.py	General file reading practice
14.SeqIO_read_genbank.py	Parse GenBank files using SeqIO
15.seqread.py	Simple sequence reading
16.Genbank_features_annotations.py	Extract features/annotations from GenBank
17.fasta_process_read.py	Process FASTA records
18.multi_fasta.py	Read multi-FASTA files
19.multi_fasta_processing.py	Filter/query multi-FASTA
20multifasta.py	Additional multi-FASTA handling
21.fasta_file.py	File I/O examples
22.Entrez_einfo.py	Use Entrez E-utilities
22.average_length_fastq.py	Calculate average read length
23.Esearch.py	NCBI ESearch examples
24.Efetch.py	Retrieve sequence using Entrez efetch
25.fetch_genbank.py	Fetch GenBank record from NCBI
26.retrive_id_and_seq.py	Fetch sequence by accession
27.py	Entrez Dataset
28.esummary.py	Entrez esummary usage
3.rna_seq1.py	RNA → Protein transformations
4.translate.py	DNA translation
5.translate_multiline.py	Translate multi-line sequences
6.open_read_frames.py	Identify ORFs and reading frames
7multiline_orf.py	ORF extraction for multi-line DNA
8.SeqUtils.py	Using Biopython SeqUtils
9.SeqUtils.py	GC content, molecular weight, etc.
nucleotide_occupance.py	Nucleotide frequency/counts

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🧬 What You Can Learn Here

By exploring these scripts, you will learn how to:

• Handle biological sequences using Python
• Parse FASTA/FASTQ/GenBank formats
• Use Biopython’s Seq, SeqRecord, and SeqIO modules
• Access NCBI databases programmatically
• Translate, reverse complement, and manipulate sequences
• Identify ORFs and coding regions
• Compute biological statistics (GC content, length, codon usage)

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Requirements

Install Biopython:

pip install biopython