The program starts with a FASTA file, BLASTs it against the database of choice, and then contrast the hits of the BLAST search against our databases to determine whether the sequence is harmful or not. Note that you can choose which database to run the BLAST search against by manipulating String[] command, which is initialized at the beginning src/main/java/Main.java
In order to run this program, you will need to have a subset of the NCBI BLAST databases downloaded on your machine. To learn more about using the BLAST tool (and NCBI databases) on your local machine, navigate through this link.