Karlin-Altschul statistics is much more than a way to determine the statistical significance of a sequence alignment in the context of a database search. It also provides a framework with which to probe the complex relationships that exist between BLAST parameters and results. Using Karlin-Altschul statistics to ask and answer questions about a BLAST search is much like using stoichiometry at the lab bench; it doesn't require theoretical savvy, just a little algebra. It's also useful; you no longer need to be frustrated when confronted with an inexplicable BLAST result.

Now let's look at a practical application of Karlin-Altschul statistics: using BLASTN to map a PCR primer to a genome. The application is a simple but striking example of how to use Karlin-Altschul statistics to understand the way parameter choice determines BLAST results. Finally, Karlin-Altschul statistics reveal much about BLASTN's strengths and weaknesses and its potential as a tool to detect the conserved, cis-regulatory regions of genes.