Nucleotide Alignment - Needleman Wunsch

Version: 2.0.0

Authors: Andrew Quach and Tamir Enkhjargal

Introduction

The repository contains a quick java implementation of aligning nucleotide sequences utilizing the Needleman-Wunsh algorithm. This was done as a project for Computer Science A as an example of dynamic programming.

Usage

Create a NeedlemanWunsch.java object. See constructors for more information.

// Two strands
NeedlemanWunsch n1 = new NeedlemanWunsch("ABC", "CAB");
// Two strands + no mismatching allowed
NeedlemanWunsch n2 = new NeedlemanWunsch("ABC", "CAB", false);
// Two strands + different MATCH/MISMATCH/INDEL scoring system
NeedlemanWunsch n3 = new NeedlemanWunsch("ABC", "CAB", 2, -2, -1);
// Two strands + different MATCH/MISMATCH/INDEL scoring system + no mismatching allowed
NeedlemanWunsch n4 = new NeedlemanWunsch("ABC", "CAB", 2, -2, -1, false);

Call methods on the object.

// Prints out aligned strands and alignment score
n1.printStrandInfo();
// Get score
n2.getScore();
// Get solution matrix
n3.getSolution();
// Get alignedStrands;
n4.getAlignedStrands();

Compile and run the java files. See the example Main.java.

javac *.java
java Main

License

This java implementation is released under the MIT License.