Looking for prophages in bacterial genomes? We added the prophage estimation tool ProphET described by Reis-Cunha et al. to CPT Galaxy. The tool uses similarity to a database of prophage genes and calculations of density and boundaries to make its determination.
To use ProphET in Galaxy, users need to supply a matched bacterial genome in nucleotide FASTA and GFF3 formats. Two files will be returned: a multifasta of each predicted prophage region, and an .svg graphic depicting where those lie within the genome. Happy hunting!
Added by Anthony Criscione, the ProphET tool can be found in the Comparative Genomics and Visualization section under Genome Visualization. Please email the support team if you have any questions!