Break Sites Prediction

SSBlazer can accurately predict the probability of single strand breaks at each nucleotide position within a DNA sequence provided in FASTA format.

Running Prediction

In order to annotate Single-Strand Break (SSB) sites on a genome, you can utilize the genome_pred.py script that is included in our toolset. This script reads in a FASTA file, performs the prediction of SSB sites, and outputs these predictions in BED format:

python genome_pred.py --in chr1.fa --out chr1_annotated.bed --batchsize 128

In this command:

• --in chr1.fa specifies the input FASTA file for the genome to be annotated.

• --out chr1_annotated.bed specifies the output BED file where the annotations will be written.

• --batchsize 128 sets the batch size to 128 for processing. You can adjust this value depending on the available resources on your machine.

The script will run and output a BED file (chr1_annotated.bed in this case) containing predicted break probabilities for the supplied genome.

Visualizing the Output

You can visualize the BED file output using Integrative Genomics Viewer (IGV). IGV is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.

Follow the instructions on the IGV website to install the software if you haven't already done so, and then load your BED file to view the annotated SSB sites on your genome.