CAUTION: the repetitive nature of many biological sequences (particularly naive translations of DNA/RNA) violates assumptions made in the Karlin & Altschul theory. While the P values provided by BLAST are a good rule-of-thumb for initial identification of promising matches, care should be taken to ensure that matches are not due simply to biased amino acid composition.
CAUTION: The databases are contaminated with numerous artifacts. The intelligent use of filters can reduce problems from these sources. Remember that the statistical theory only covers the likelihood of finding a match by chance under particular assumptions; it does not guarantee biological importance.