Needleman-Wunsch Algorithm Project

Overview

This project implements the Needleman-Wunsch algorithm, a classic method for global sequence alignment. It is widely used in bioinformatics to align protein or nucleotide sequences, scoring matches, mismatches, and gaps based on a predefined scoring system.

The program reads a CSV file containing pairs of sequences, aligns them using the Needleman-Wunsch algorithm, and outputs the aligned sequences along with their alignment scores.

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Features

1. Global Sequence Alignment:

   • Computes the optimal alignment of two sequences based on a scoring matrix and gap penalties.
   • Outputs aligned sequences and the alignment score.

2. Customizable Scoring:

   • Match score: +1.
   • Mismatch penalty: -1.
   • Gap penalty: -2.

3. CSV File Integration:

   • Reads pairs of sequences from a CSV file for alignment.

4. Alignment Output:

   • Outputs aligned sequences and their alignment scores to the console.

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Files in the Project

1. needleman_wunsch.py: The primary Python script containing the Needleman-Wunsch implementation.
2. Input file (CSV): A file containing pairs of sequences for alignment (e.g., sequences.csv).

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Installation and Usage

Prerequisites

• Python 3.7 or higher.
• The csv module (built into Python).
• A terminal or command-line interface.

Running the Project

1. Prepare the input file:

   • Create a CSV file where each row contains a pair of sequences to be aligned.
   • Example format:

     Sequence1,Sequence2
     AGCT,AGTT
     GAT,CTT
     

2. Run the script:

   python needleman_wunsch.py <input_file>