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Phage sequences in bacterial genomes
The truth behind Blast
The Bacteriophage P2
Certain bacterial viruses (called bacteriophages) carry with them extra genes, which play no role in viral function. In some cases, the extra DNA encodes virulence factors, proteins that can make the difference between harmless and pathogenic bacteria. You are studying the bacteriophage P2, which is known to insert itself into bacterial genomes as prophages. Some P2-like phages carry virulence genes.
How frequently are P2-like phage (and the genes they bring with them) found in bacterial genomes? To find out, you've decided to screen DNA from a variety of bacteria for the presence of DNA sequences from P2-like phage. Your plan is to amplify P2 sequences from bacterial DNA, using primers designed to specifically recognize P2 DNA. It's important that the primers recognize DNA from all P2-like phage but not bacterial DNA.
How do you find primers you're confident will recognize all P2-like phage?
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