🧬 BioSeqAlign - DNA Sequence Alignment in Java

📖 Overview

BioSeqAlign is a Java-based tool for aligning DNA sequences using Dynamic Programming.
It identifies the Longest Common Subsequence (LCS) between two DNA strands, highlighting similarities that may indicate functional or evolutionary relationships.

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✨ Features

• Implements the Longest Common Subsequence (LCS) algorithm.
• Efficient sequence alignment using dynamic programming.
• Clear console output with subsequence and length.

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⚙️ Installation & Execution

1. Clone this repository:

   git clone https://github.com/Dakarplay/BioSeqAlign.git
   cd BioSeqAlign
   

2. Compile the project

   javac -d bin src/lib/LCS.java src/App.java

3. Run the program:

   java -cp bin App

🖥️ Usage

The input DNA sequences are defined in App.java. Modify the variables X and Y to test different alignments.

Example

Input:

- Sequence 1: ACTGAAAAATTTTTTTTTTTTTCCGGGGGGGGGGAAAAAAA
- Sequence 2: TCAAGGGGGTCAAAAAAAAAAACGTGA

Output:

- Longest Common Subsequence: TAAGGGGGAAAAAAA
- Length of the LCS: 15

📊 Complexity Analysis

- Time Complexity: O(m * n)

- Space Complexity: O(m * n)

Where m and n are the lengths of the input sequences.

Author

Developed by Dago Palmera