VCU Bioinformatics and Bioengineering Summer Institute
Virginia Commonwealth University
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Research Simulation Scenario
Phage sequences in bacterial genomes
The truth behind Blast

Quality control: Are primer sequences in bacterial genome?

The primers are useful so long as they don't recognize DNA from bacteria without P2-like prophages. You can't check every conceivable host bacterium, but you can at least check DNA from one: E. coli K12. Its genome has been sequenced, and P2 is demonstrably not there. It's now a simple (?) matter to determine whether the primers are found in the K12 genome. If not, they should be useful for the task at hand.

Fortunately, there is a publically accessible program, BLAST, that seems perfect for the job. BLAST compares sequences you input to a database of sequences. Use BLAST to run the primer sequences through the K12 genome. If a lengthy match to the genome is found, then the primer sequence will need to be thrown out.

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