Biotech > FAQ > BLAST FAQ (Frequently Asked Questions)

After running a search why do I see a st...

To see other biotech frequently asked questions, please visit

(Continued from previous question...)

After running a search why do I see a string of "X"s (or "N"s) in my query sequence that I did not put there?

You are seeing the result of automatic filtering of your query for low-complexity sequence that is performed to prevent artifactual hits. The filter substitutes any low-complexity sequence that it finds with the letter "N" in nucleotide sequence (e.g., "NNNNNNNNNNNNN") or the letter "X" in protein sequences (e.g., "XXXXXXXXX"). Low-complexity regions can result in high scores that reflect compositional bias rather than significant position-by-position alignment (Wootton amp; Federhen, 1996). Filter programs can eliminate these potentially confounding matches from the blast reports, leaving regions whose BLAST statistics reflect the specificity of their parities alignment. Queries searched with the blastn program are filtered with DUST. The other BLAST programs use SEG.

(Continued on next question...)

Other Frequently Asked Questions