DNAAT Usage Guide

Running DNAAT

DNAAT is run from the command line using the main dnaat.py wrapper. This single entry point allows you to choose your alignment method and customize the parameters.

1. Setup

First, clone the DNAAT repository from GitHub and navigate into the project directory:

git clone https://github.com/no1berg/DNAAT.git
cd dnaat

2. Basic Usage

The main script dnaat.py uses commands to select the alignment type. You must specify either global or local.

Global Alignment

To perform a global alignment on two sequences from a FASTA file:

python dnaat.py global path/to/your/sequences.fasta

Local Alignment

To perform a local alignment on two sequences from a FASTA file:

python dnaat.py local path/to/your/sequences.fasta

3. Customizing Scores

You can customize the alignment scores using optional arguments. These work for both global and local commands.

• --match: Sets the score for a match (default: 1).
• --mismatch: Sets the score for a mismatch (default: -1).
• --gap: Sets the gap penalty (default: -2).

Example:

python dnaat.py global your_sequences.fasta --match 5 --mismatch -3 --gap -4

4. Using Example Data

If you run a command without providing a file path, the tool will use built-in example sequences.

python dnaat.py local

5. Performance Testing

To benchmark the C-accelerated functions against the pure Python implementation, you can still run the dedicated test script:

python test_performance.py