MohamedAboSaleh/Cracking-The-DNA-Protein-Binding-Code — reverse-engineered prompt

Build me a Java desktop app for a bioinformatics research project called Cracking The DNA Protein Binding Code.

I want a simple JavaFX GUI where a user can choose a DNA sequence file and a DNA binding sites file, then pick one of several analysis methods and run it. The app should analyze DNA around binding sites using sliding windows, compare word frequencies and reverse complements, and show possible pointer sequences that may guide DNA binding proteins.

Please include the main algorithms described in the README, segmented DNA analysis, word occurrence comparison, segmented word distribution, and PWM based scoring. The results should be easy to view in the app, with enough details like the candidate sequence, counts or score, direction, and why it was flagged.

Keep it practical and academic, not flashy. Add clear sample input expectations, helpful error messages for bad files, and a simple way to run the project locally with Java and JavaFX.