PhiSpy can be used to identify the prophage regions in your prokaryotic genome.

Example files:
  Escherichia_coli_K12.gb
  g.0.gbk
  g.100.gbk


The paper for PhiSpy is available at: http://nar.oxfordjournals.org/content/40/16/e126



Fasta format files of prophage predictions from 11,278 Bacterial and Archaeal genomes. Each fasta file is labeled with the NCBI taxonomy ID of the organism and the name of the organism, and each entry in the fasta file is one prophage prediction.

     PhiSpy_Prophage_Predictions.zip
     There are 9,086 genome files and each file has the prophages predicted for a different genome.