GenomeIndexing

Overview

The GenomeIndexing is a Java tool for extracting indices and seeds from genome sequences using Minimizer and Genome-on-Diet algorithms. This project apply the concepts explained in this lecture, which is part of the Introduction to Bioinformatics course taught at the Islamic University of Gaza (IUG).

Input file structure

• The first line of the input contains one integer n — the number of test cases.

• Each test case consists of three lines:

  • The first line of each test case contains one integer t — the type of the algorithm to be used on the following genome sequence. This project covers only two types:

    1. Minimizer, t must be 1.
    2. Genome-on-Diet, t must be 2.

  • The second line contains the genome sequence.

  • The third line contains the integers k, w, and p (if applicable) respectively.

Example: sample-input.txt

Prerequisites

To run this project, you need:

• Java Development Kit (JDK) 18 or later installed.
• An IDE (e.g., IntelliJ IDEA, Eclipse, or VS Code) or the command line for running Java applications.

Project Setup

You can install To run this project, follow these steps:

1. Clone the repository:

   git clone https://github.com/MohammedOH/GenomeIndexing.git
   cd GenomeIndexing

2. Create the input file, and follow the Input file structure:

    touch input.txt

   or

    echo "" > input.txt

   For more help see sample-input.txt file

3. Compile the Project:

   javac -source 18 -target 18 -d out src/*.java

4. Run the Project:

   java -cp out Main

5. Open the output file output.txt.

License

This project is licensed under the MIT License.

Created By

Mohammed O. AlHabbash,
mohammad.o.a1999@gmail.com