8.8 Mask Repeats in Genomic DNA

As mentioned in Chapter 2, genomes may be full of repetitive elements and low-complexity sequence. They can be very problematic in BLAST searches, and if not masked prior to a BLAST search, will waste computer time and inflate BLAST reports with meaningless, redundant information (Figure 8-4).

Figure 8-4. BLASTX search with (a) repeats intact and (b) repeats masked (the alignments were removed from the display)